MolNFT v1 · #52331 · protein
Crystal structure of pa-il lectin complexed with AGAL13BGAL14GLC at 1.9 a resolution
2VXJ · Pa-I galactophilic lectin: “Crystal structure of pa-il lectin complexed with AGAL13BGAL14GLC at 1.9 a resolution”. X-ray diffraction, 5 ligands (GAL, GLA, BGC), 20 pockets (best druggability 0.81). MolNFT v1 #52331 on GenesisL1: 3D…
- PDB
- 2VXJ
- Type
- protein
- Length
- 2,896 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pa-I galactophilic lectin
- UniProt
- Q05097
- Ligands
- GAL, GLA, BGC, GLC, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, G, H, I, K, L, M, O, P, Q, R, S, T, U, V, W, X | Pa-I galactophilic lectin | protein | 121 | 2% helix, 45% strand | Q05097 |
| B | Pa-I galactophilic lectin | protein | 118 | 3% helix, 52% strand | Q05097 |
| C | Pa-I galactophilic lectin | protein | 119 | 3% helix, 50% strand | Q05097 |
| D, N | Pa-I galactophilic lectin | protein | 120 | 3% helix, 49% strand | Q05097 |
| J | Pa-I galactophilic lectin | protein | 120 | 0% helix, 46% strand | Q05097 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- GLA · alpha-D-galactopyranose · sugar · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- BGC · beta-D-glucopyranose · sugar · 22 copies · chains A, B, D, F, G, H, I, J, K, L, M, O, P, Q, R, S, T, U, V, W, X, N
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains C, E
- CA · Calcium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, Q, O, P, R, U, S, T, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.81 | 0.82 | 100 | empty |
| 2 | 1172 | 0.81 | 0.82 | 95 | empty |
| 3 | 1156 | 0.80 | 0.82 | 96 | empty |
| 4 | 952 | 0.72 | 0.76 | 83 | empty |
| 5 | 947 | 0.72 | 0.76 | 82 | empty |
Interfaces
57 interfaces between chains.
- Q–R · 1104 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1088 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 1086 Ų buried · 9 hydrogen bonds · protein-protein
- U–V · 1084 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1083 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2VXJ · Crystal structure of pa-il lectin complexed with AGAL13BGAL14GLC at 1.9 a resolution · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q05097
- Elsewhere: RCSB PDB 2VXJ · PDBe 2VXJ · UniProt Q05097
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