MolNFT v1 · #74922 · protein
Crystal structure of a putative adhesin (BACOVA_04077) from bacteroides ovatus at 2.50 a resolution
3PAY: “Crystal structure of a putative adhesin (BACOVA_04077) from bacteroides ovatus at 2.50 a resolution”. X-ray diffraction, 15 pockets (best druggability 0.78). MolNFT v1 #74922 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3PAY
- Type
- protein
- Length
- 1,231 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative adhesin
- UniProt
- A7M1U3
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative adhesin | protein | 302 | 8% helix, 44% strand | A7M1U3 |
| B | Putative adhesin | protein | 309 | 7% helix, 44% strand | A7M1U3 |
| C | Putative adhesin | protein | 307 | 8% helix, 44% strand | A7M1U3 |
| D | Putative adhesin | protein | 313 | 8% helix, 44% strand | A7M1U3 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.78 | 0.80 | 114 | empty |
| 2 | 243 | 0.57 | 0.78 | 38 | empty |
| 3 | 150 | 0.48 | 0.77 | 28 | empty |
| 4 | 159 | 0.48 | 0.77 | 26 | empty |
| 5 | 110 | 0.45 | 0.78 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1138 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1097 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 899 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 311 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 3PAY · Crystal structure of a putative adhesin (BACOVA_04077) from Bacteroides ovatus at 2.50 A… · the same entry in another collection · chain A against A, 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 A7M1U3
- Elsewhere: RCSB PDB 3PAY · PDBe 3PAY · UniProt A7M1U3
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