MolNFT v1 · #72120 · protein
Crystal structure of a susd superfamily protein (BVU_0732) from bacteroides vulgatus atcc 8482 at 1.80 a resolution
3MYV: “Crystal structure of a susd superfamily protein (BVU_0732) from bacteroides vulgatus atcc 8482 at 1.80 a…”. X-ray diffraction, 2 ligands (NA, PO4), 8 pockets (best druggability 0.75). MolNFT v1 #72120 on GenesisL1: 3D structure…
- PDB
- 3MYV
- Type
- protein
- Length
- 889 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Susd superfamily protein
- UniProt
- A6KYC4
- Ligands
- NA, PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Susd superfamily protein | protein | 445 | 49% helix, 10% strand | A6KYC4 |
| B | Susd superfamily protein | protein | 444 | 49% helix, 10% strand | A6KYC4 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.75 | 0.98 | 25 | EDO |
| 2 | 72 | 0.73 | 0.97 | 24 | EDO |
| 3 | 399 | 0.72 | 0.83 | 48 | EDO, PO4 |
| 4 | 151 | 0.47 | 0.77 | 22 | EDO |
| 5 | 92 | 0.42 | 0.78 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 615 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 3MYV · Crystal structure of a SusD superfamily protein (BVU_0732) from Bacteroides vulgatus ATCC… · 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 A6KYC4
- Elsewhere: RCSB PDB 3MYV · PDBe 3MYV · UniProt A6KYC4
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