MolNFT v1 · #104526 · protein
Crystal structure of a putative adhesin (BT2657) from bacteroides thetaiotaomicron vpi-5482 at 2.20 a resolution (psi community target, nakayama)
4QDG: “Crystal structure of a putative adhesin (BT2657) from bacteroides thetaiotaomicron vpi-5482 at 2.20 a…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.35). MolNFT v1 #104526 on GenesisL1: 3D structure, binding…
- PDB
- 4QDG
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative adhesin
- UniProt
- Q8A4E2
- Ligands
- MG
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative adhesin | protein | 300 | 12% helix, 44% strand | Q8A4E2 |
| B | Putative adhesin | protein | 302 | 12% helix, 44% strand | Q8A4E2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.35 | 0.72 | 13 | empty |
| 2 | 78 | 0.33 | 0.75 | 18 | empty |
| 3 | 54 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 146 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 4QDG · Crystal structure of a putative adhesin (BT2657) from Bacteroides thetaiotaomicron… · 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 Q8A4E2
- Elsewhere: RCSB PDB 4QDG · PDBe 4QDG · UniProt Q8A4E2
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