Unified Binding Sites

P00918 Carbonic anhydrase 2 Homo sapiens
UniProtKB AlphaFold PDBe InterPro
603binding sites 2374AHoJ-DB entries 5thresholds 2116holo /257apo

How to read this page

Unified binding site
Each entry's binding site is its set of binding residues, in UniProt numbering. Two sites are compared by Jaccard similarity: the residues they share, divided by the residues of both together. This protein's entries are clustered hierarchically on that similarity (average linkage) and the tree is cut at the threshold; every branch below the cut is one unified site, whose members' sites are on average at least that similar to one another. Each table row is one unified site: Site counts the core residues every member shares (core / union when members differ), Entries the DB entries in it. Hover any cell for the details.
AHoJ-DB entry
One ligand bound to one PDB chain, named pdb-chain-ligand-residue (e.g. 1bab-A-HEM-143: entry 1bab, chain A, heme 143), with the apo and holo structures AHoJ found for that site. This protein's entries are the members of the unified sites and the leaves of the dendrogram.
Threshold
The Jaccard similarity at which the tree is cut. 0.30 gives few, broad sites; 1.00 keeps only identical residue sets together; the page opens on 1.00. LJ is the cut chosen automatically at the largest linkage jump of the dendrogram.
Homologs, interfaces
A unified site can span homologous UniProts (the ×N badge; hover for the list), so its AlphaFold votes may outnumber this protein's entries. ⧉ marks a site at a protein–protein interface.
AlphaFold class
Whether the AlphaFold model of this protein resembles the apo (A) or the holo (H) structures at the site, judged on the pocket; ? = undefined, — = no AlphaFold data. Hover the chip for the pocket- and chain-level breakdown.
Confidence
The probability of the winning class, max(P(apo), P(holo)); the bar fills from white to the class colour.
Density
How close the model sits to the observed structures: 1 = at their peak, 0 = an outlier.
Separation
How distinguishable the apo and holo structures are, 1 − overlap of their distributions: 1 = disjoint, 0 = identical. A classification means little where separation is low; it is blank when one state has no structures.
Apo : Holo
How AlphaFold classifies the site's members (apo, holo). The header strip sums these votes over every site of the threshold the page opens on.
Representative
The exemplar member of a site, shown in indigo in its entries list and in the UBS card; click a cell to pin its card and follow the links.
Binding positions
For each residue of the UniProt sequence, the share (left axis) and number (right axis) of this protein's entries whose binding site includes it; light bars are single-chain sites, blue bars interface sites. The peaks are the protein's recurrent binding sites.
Dendrogram
The clustering tree behind the unified sites. Each leaf is one entry (click to open; the bracket is its number of binding residues), branches join at the similarity on the axis, the dashed lines are the thresholds, and the branches right of a line are that threshold's unified sites, labelled core / union residues.
binding positions · dendrogram

Loading dendrogram for P00918...

Hierarchical clustering (average linkage) of this protein's AHoJ-DB entries by the Jaccard similarity (%) of their binding-residue sets.

  • Leaves: one DB entry each (click one to open it); the number in brackets is its count of binding residues.
  • Dashed lines: the thresholds. The one selected in the table below is highlighted and the others fade; 1.00's lies on the leaves.
  • Branches to the right of a line: that threshold's unified sites, labelled with their core / union residue counts.

Loading binding positions for P00918...

How often each residue of the UniProt sequence is part of a binding site across this protein's entries: the share of entries on the left axis, their count on the right.

  • Light bars: single-chain sites; blue bars: interface sites (two or more chains).
  • Click the plot to enlarge it.
P00918: binding positions
Binding positions of P00918, enlarged
Binding sites at thresholdClustering threshold Jaccard similarity cut on the binding-residue sets of this UniProt's entries, used to merge them into unified sites. Lower = broader (more sites merged); higher = stricter; 1.00 merges only identical residue sets. LJ is a cut picked automatically at the largest jump in the same tree (UniProts with ≥3 entries only).:
Loading binding sites…
Loading binding sites…
Loading binding sites…
Threshold: 1.0
Cluster AlphaFold model (unified site)
UBS Unified Binding Site Cluster of this UniProt's binding sites merged at this threshold (Jaccard similarity of residue sets). ⧉ marks a binding site at a protein–protein interface. Site Site size (residues) Number of core residues shared by all cluster members. A second number (core / union) appears when the union across members is larger. Hover a cell for the residue list. Entries AHoJ-DB entries Structures assigned to this cluster. Hover for the list — each links to its DB entry. Class AlphaFold classification Predicted state (H holo, A apo, ? undefined, — no AlphaFold data) of the unified binding site — this site merged across its homologs, which may span several UniProts. Hover for P(apo)/P(holo), votes, density, separation and the chain-level values. Confidence Classification confidence Probability of the winning AF class for the unified site, max(P(apo), P(holo)), averaged over the pocket metrics and the site's members. The bar fills from white to the class colour (blue apo, red holo, as in the violin plots); — when the site has no AlphaFold probabilities. Density Normalised density Density of the observed apo + holo structures at the AlphaFold model's position, averaged over the pocket metrics and the site's members: 1 = the model sits at the peak of the observed distribution, 0 = it is an outlier. Hover a cell for the chain-level value. Separation Apo / holo separation How distinguishable the apo and holo distributions are: 1 − overlap, averaged over the overall and the mode (peak) overlap, the pocket metrics and the site's members. 1 = disjoint, 0 = identical, so a classification means little where this is low. Hover a cell for the chain-level value. Apo:Holo AF apo : holo votes How the unified site's members are classified by AlphaFold (blue apo, red holo, as in the violin plots). Votes span all homologous members across UniProts, so the total can exceed this row's Entries count.
#1 6 1 A0.61
0.61
 0.60 0.07
1:0 A:H
#2 7 1 A0.63
0.63
 0.59 0.07
1:0 A:H
#3 5 1 A0.65
0.65
 0.42 0.07
1:0 A:H
#4 7 1 A0.53
0.53
 0.32 0.06
1:0 A:H
#5 8 2 A0.60
0.60
 0.28 0.51
2:0 A:H
#6 7 1 A0.68
0.68
 0.33 0.24
1:0 A:H
#7 7 1 A0.57
0.57
 0.57 0.50
1:0 A:H
#8 5 1 A0.73
0.73
 0.66 0.47
1:0 A:H
#9 5 1 A0.63
0.63
 0.52 0.28
1:0 A:H
#10 6 1 H0.80
0.80
 0.50 0.26
0:1 A:H
#11 37 1 A0.53
0.53
 0.87 0.28
1:0 A:H
#12 15 1 H0.52
0.52
 0.70 0.14
0:1 A:H
#13 7 3 A0.52
0.52
 0.45 0.20
3:0 A:H
#14 6 1 A0.54
0.54
 0.40 0.33
1:0 A:H
#15 8 2 H0.61
0.61
 0.41 0.23
0:2 A:H
#16 9 1 H0.67
0.67
 0.40 0.25
0:1 A:H
#17 7 4 H0.57
0.57
 0.29 0.35
0:4 A:H
#18 6 1 H0.64
0.64
 0.57 0.54
0:1 A:H
#19 4 10 A0.55
0.55
 0.57 0.33
10:0 A:H
#20 5 2 A0.64
0.64
 0.47 0.64
2:0 A:H
#21 4 3 H0.65
0.65
 0.51 0.22
0:3 A:H
#22 5 898 H0.63
0.63
 0.55 0.38
1:897 A:H
#23 6 1 H0.66
0.66
 0.54 0.36
0:1 A:H
#24 5 2 A0.53
0.53
 0.61 0.19
2:0 A:H
#25 6 183 H0.64
0.64
 0.59 0.28
0:183 A:H
#26 7 1 H0.50
0.50
 0.56 0.15
0:1 A:H
#27 7 1 H0.65
0.65
 0.62 0.30
0:1 A:H
#28 4 1 H0.66
0.66
 0.57 0.23
0:1 A:H
#29 18 1 H0.78
0.78
 0.26 0.32
0:1 A:H
#30 16 1 H0.76
0.76
 0.55 0.33
0:1 A:H
#31 11 1 H0.64
0.64
 0.23 0.24
0:1 A:H
#32 12 1 H0.71
0.71
 0.35 0.24
0:1 A:H
#33 11 1 H0.84
0.84
 0.22 0.38
0:1 A:H
#34 10 1 H0.78
0.78
 0.21 0.34
0:1 A:H
#35 13 6 H0.59
0.59
 0.45 0.45
0:6 A:H
#36 12 1 H0.85
0.85
 0.26 0.27
0:1 A:H
#37 13 1 H0.85
0.85
 0.26 0.35
0:1 A:H
#38 12 1 H0.81
0.81
 0.23 0.34
0:1 A:H
#39 12 1 H0.75
0.75
 0.53 0.41
0:1 A:H
#40 9 4 H0.85
0.85
 0.21 0.34
0:4 A:H
#41 10 3 H0.88
0.88
 0.25 0.34
0:3 A:H
#42 10 1 H0.92
0.92
 0.20 0.32
0:1 A:H
#43 8 1 H0.75
0.75
 0.22 0.28
0:1 A:H
#44 8 1 H0.64
0.64
 0.51 0.47
0:1 A:H
#45 12 1 H0.81
0.81
 0.28 0.41
0:1 A:H
#46 10 1 H0.72
0.72
 0.30 0.29
0:1 A:H
#47 12 1 H0.81
0.81
 0.32 0.49
0:1 A:H
#48 22 1 H0.63
0.63
 0.50 0.44
0:1 A:H
#49 23 1 A0.57
0.57
 0.34 0.43
1:0 A:H
#50 21 1 H0.63
0.63
 0.49 0.41
0:1 A:H
#51 27 1 H0.59
0.59
 0.48 0.38
0:1 A:H
#52 15 1 A0.51
0.51
 0.40 0.41
1:0 A:H
#53 17 1 H0.61
0.61
 0.40 0.43
0:1 A:H
#54 18 1 H0.54
0.54
 0.44 0.44
0:1 A:H
#55 20 1 H0.72
0.72
 0.30 0.22
0:1 A:H
#56 21 1 H0.54
0.54
 0.46 0.40
0:1 A:H
#57 19 1 H0.64
0.64
 0.31 0.38
0:1 A:H
#58 19 1 H0.60
0.60
 0.38 0.37
0:1 A:H
#59 20 1 H0.56
0.56
 0.36 0.41
0:1 A:H
#60 20 1 H0.53
0.53
 0.45 0.42
0:1 A:H
#61 18 1 H0.52
0.52
 0.54 0.27
0:1 A:H
#62 16 1 H0.65
0.65
 0.34 0.20
0:1 A:H
#63 17 1 H0.54
0.54
 0.39 0.41
0:1 A:H
#64 12 1 H0.74
0.74
 0.25 0.27
0:1 A:H
#65 14 1 H0.78
0.78
 0.23 0.27
0:1 A:H
#66 17 1 H0.70
0.70
 0.17 0.34
0:1 A:H
#67 14 1 H0.78
0.78
 0.28 0.36
0:1 A:H
#68 8 3 H0.53
0.53
 0.58 0.27
0:3 A:H
#69 9 1 H0.66
0.66
 0.52 0.39
0:1 A:H
#70 7 1 H0.51
0.51
 0.63 0.26
0:1 A:H
#71 10 1 H0.56
0.56
 0.34 0.28
0:1 A:H
#72 9 1 H0.63
0.63
 0.34 0.23
0:1 A:H
#73 9 2 A0.51
0.51
 0.43 0.14
2:0 A:H
#74 8 1 H0.55
0.55
 0.47 0.14
0:1 A:H
#75 10 2 H0.72
0.72
 0.36 0.27
0:2 A:H
#76 9 2 H0.61
0.61
 0.55 0.30
0:2 A:H
#77 11 1 H0.63
0.63
 0.45 0.21
0:1 A:H
#78 12 1 H0.68
0.68
 0.44 0.21
0:1 A:H
#79 9 2 H0.67
0.67
 0.56 0.14
0:2 A:H
#80 10 3 H0.60
0.60
 0.52 0.14
0:3 A:H
#81 12 4 H0.69
0.69
 0.39 0.27
0:4 A:H
#82 11 1 H0.71
0.71
 0.40 0.22
0:1 A:H
#83 10 5 H0.69
0.69
 0.40 0.20
0:5 A:H
#84 11 8 H0.70
0.70
 0.48 0.24
0:8 A:H
#85 12 1 H0.72
0.72
 0.31 0.30
0:1 A:H
#86 9 1 H0.55
0.55
 0.35 0.27
0:1 A:H
#87 11 1 H0.58
0.58
 0.38 0.20
0:1 A:H
#88 10 1 H0.60
0.60
 0.45 0.27
0:1 A:H
#89 10 1 H0.56
0.56
 0.51 0.22
0:1 A:H
#90 8 1 A0.53
0.53
 0.57 0.17
1:0 A:H
#91 12 1 H0.55
0.55
 0.42 0.28
0:1 A:H
#92 11 1 H0.58
0.58
 0.45 0.32
0:1 A:H
#93 11 1 A0.56
0.56
 0.54 0.29
1:0 A:H
#94 14 2 H0.76
0.76
 0.60 0.47
0:2 A:H
#95 15 1 H0.71
0.71
 0.46 0.53
0:1 A:H
#96 18 1 H0.74
0.74
 0.64 0.34
0:1 A:H
#97 16 1 H0.63
0.63
 0.47 0.30
0:1 A:H
#98 16 1 A0.53
0.53
 0.52 0.45
1:0 A:H
#99 13 1 H0.86
0.86
 0.38 0.27
0:1 A:H
#100 12 1 H0.68
0.68
 0.35 0.27
0:1 A:H
#101 10 1 H0.64
0.64
 0.28 0.28
0:1 A:H
#102 11 1 H0.79
0.79
 0.32 0.32
0:1 A:H
#103 11 1 H0.83
0.83
 0.34 0.23
0:1 A:H
#104 9 1 H0.57
0.57
 0.41 0.42
0:1 A:H
#105 10 1 H0.84
0.84
 0.32 0.23
0:1 A:H
#106 10 2 H0.64
0.64
 0.46 0.38
0:2 A:H
#107 11 4 H0.63
0.63
 0.57 0.34
0:4 A:H
#108 12 1 H0.63
0.63
 0.46 0.29
0:1 A:H
#109 12 3 H0.61
0.61
 0.30 0.21
0:3 A:H
#110 11 1 H0.70
0.70
 0.44 0.32
0:1 A:H
#111 11 6 H0.80
0.80
 0.32 0.20
0:6 A:H
#112 12 1 H0.69
0.69
 0.30 0.23
0:1 A:H
#113 12 1 H0.64
0.64
 0.31 0.25
0:1 A:H
#114 11 1 H0.85
0.85
 0.35 0.24
0:1 A:H
#115 14 2 H0.66
0.66
 0.35 0.21
0:2 A:H
#116 13 5 H0.65
0.65
 0.37 0.20
0:5 A:H
#117 14 1 H0.72
0.72
 0.50 0.26
0:1 A:H
#118 12 4 H0.83
0.83
 0.35 0.22
0:4 A:H
#119 11 2 H0.86
0.86
 0.33 0.26
0:2 A:H
#120 11 1 A0.51
0.51
 0.38 0.20
1:0 A:H
#121 11 1 H0.82
0.82
 0.30 0.23
0:1 A:H
#122 10 1 H0.82
0.82
 0.29 0.26
0:1 A:H
#123 9 3 H0.64
0.64
 0.49 0.35
0:3 A:H
#124 8 1 H0.58
0.58
 0.55 0.38
0:1 A:H
#125 10 1 H0.86
0.86
 0.31 0.23
0:1 A:H
#126 11 1 H0.56
0.56
 0.48 0.41
0:1 A:H
#127 9 1 H0.86
0.86
 0.27 0.28
0:1 A:H
#128 18 4 H0.64
0.64
 0.33 0.32
0:4 A:H
#129 18 1 H0.57
0.57
 0.49 0.24
0:1 A:H
#130 16 1 H0.70
0.70
 0.34 0.24
0:1 A:H
#131 17 2 H0.83
0.83
 0.36 0.16
0:2 A:H
#132 18 1 H0.83
0.83
 0.35 0.17
0:1 A:H
#133 19 1 H0.76
0.76
 0.42 0.20
0:1 A:H
#134 18 1 H0.55
0.55
 0.49 0.23
0:1 A:H
#135 22 1 H0.76
0.76
 0.50 0.17
0:1 A:H
#136 14 2 H0.74
0.74
 0.44 0.35
0:2 A:H
#137 13 3 H0.82
0.82
 0.35 0.33
0:3 A:H
#138 15 1 H0.59
0.59
 0.31 0.36
0:1 A:H
#139 15 1 H0.56
0.56
 0.29 0.37
0:1 A:H
#140 18 1 H0.73
0.73
 0.35 0.21
0:1 A:H
#141⧉ 23 1 H1.00
1.00
 0.25 —
0:1 A:H
#142⧉ 22 1 H0.89
0.89
 0.22 0.37
0:1 A:H
#143 27 1 H0.75
0.75
 0.43 0.49
0:1 A:H
#144 25 1 H0.84
0.84
 0.34 0.27
0:1 A:H
#145 22 1 H0.84
0.84
 0.52 0.34
0:1 A:H
#146 22 1 H0.84
0.84
 0.49 0.36
0:1 A:H
#147 20 1 H0.72
0.72
 0.28 0.26
0:1 A:H
#148 23 1 H0.62
0.62
 0.50 0.46
0:1 A:H
#149 19 1 H0.56
0.56
 0.58 0.51
0:1 A:H
#150 18 1 H0.79
0.79
 0.50 0.32
0:1 A:H
#151 19 1 H0.78
0.78
 0.37 0.26
0:1 A:H
#152 20 1 H0.64
0.64
 0.48 0.29
0:1 A:H
#153 18 1 H0.57
0.57
 0.52 0.24
0:1 A:H
#154 19 1 H0.54
0.54
 0.38 0.23
0:1 A:H
#155 17 1 H0.60
0.60
 0.47 0.37
0:1 A:H
#156 17 3 H0.58
0.58
 0.42 0.39
0:3 A:H
#157 16 1 H0.69
0.69
 0.54 0.43
0:1 A:H
#158 18 1 H0.53
0.53
 0.51 0.32
0:1 A:H
#159 19 1 H0.58
0.58
 0.46 0.42
0:1 A:H
#160 19 1 A0.54
0.54
 0.35 0.38
1:0 A:H
#161 15 1 H0.65
0.65
 0.49 0.40
0:1 A:H
#162 14 1 H0.64
0.64
 0.52 0.35
0:1 A:H
#163 14 1 H0.57
0.57
 0.60 0.41
0:1 A:H
#164 20 1 H0.68
0.68
 0.36 0.41
0:1 A:H
#165⧉ 22 1 H0.82
0.82
 0.20 0.31
0:1 A:H
#166⧉ 21 1 H1.00
1.00
 0.04 —
0:1 A:H
#167 20 1 H0.67
0.67
 0.55 0.35
0:1 A:H
#168 19 1 H0.87
0.87
 0.35 0.28
0:1 A:H
#169 18 1 A0.60
0.60
 0.44 0.31
1:0 A:H
#170 19 1 H0.54
0.54
 0.35 0.21
0:1 A:H
#171 19 1 A0.51
0.51
 0.41 0.32
1:0 A:H
#172 16 1 A0.51
0.51
 0.48 0.34
1:0 A:H
#173 18 6 H0.52
0.52
 0.48 0.33
0:6 A:H
#174 17 1 A0.57
0.57
 0.43 0.35
1:0 A:H
#175 17 1 H0.71
0.71
 0.48 0.34
0:1 A:H
#176 18 1 H0.51
0.51
 0.57 0.34
0:1 A:H
#177 19 1 H0.70
0.70
 0.46 0.28
0:1 A:H
#178 20 1 H0.81
0.81
 0.38 0.34
0:1 A:H
#179 20 2 H0.60
0.60
 0.46 0.42
0:2 A:H
#180 21 2 H0.69
0.69
 0.54 0.41
0:2 A:H
#181 20 1 H0.58
0.58
 0.54 0.36
0:1 A:H
#182 20 1 H0.66
0.66
 0.51 0.34
0:1 A:H
#183 20 1 H0.72
0.72
 0.31 0.25
0:1 A:H
#184 21 1 H0.60
0.60
 0.36 0.30
0:1 A:H
#185 21 1 H0.58
0.58
 0.33 0.38
0:1 A:H
#186 16 1 H0.58
0.58
 0.43 0.46
0:1 A:H
#187 17 1 H0.54
0.54
 0.39 0.38
0:1 A:H
#188 19 1 H0.57
0.57
 0.26 0.24
0:1 A:H
#189 20 1 H0.62
0.62
 0.31 0.36
0:1 A:H
#190 19 2 H0.63
0.63
 0.30 0.28
0:2 A:H
#191 20 1 H0.56
0.56
 0.40 0.28
0:1 A:H
#192 18 3 H0.57
0.57
 0.35 0.33
0:3 A:H
#193 19 1 H0.53
0.53
 0.37 0.41
0:1 A:H
#194 17 1 H0.64
0.64
 0.38 0.45
0:1 A:H
#195 21 2 H0.62
0.62
 0.41 0.28
0:2 A:H
#196 22 1 H0.61
0.61
 0.44 0.25
0:1 A:H
#197 23 1 H0.56
0.56
 0.50 0.29
0:1 A:H
#198 19 2 H0.51
0.51
 0.39 0.35
0:2 A:H
#199 18 2 H0.54
0.54
 0.37 0.41
0:2 A:H
#200 19 1 H0.61
0.61
 0.36 0.30
0:1 A:H
#201 18 2 H0.70
0.70
 0.34 0.34
0:2 A:H
#202 19 1 H0.73
0.73
 0.25 0.25
0:1 A:H
#203 19 1 H0.75
0.75
 0.27 0.29
0:1 A:H
#204 19 1 H0.64
0.64
 0.22 0.26
0:1 A:H
#205 17 1 H0.62
0.62
 0.54 0.30
0:1 A:H
#206 18 2 H0.59
0.59
 0.26 0.30
0:2 A:H
#207 19 1 H0.57
0.57
 0.27 0.24
0:1 A:H
#208 21 1 H0.56
0.56
 0.41 0.29
0:1 A:H
#209 19 1 H0.72
0.72
 0.29 0.23
0:1 A:H
#210 22 1 H0.69
0.69
 0.26 0.42
0:1 A:H
#211 17 2 H0.58
0.58
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0:2 A:H
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