MolNFT v1 · #77785 · protein
The crystal structure of a possible metal-dependent hydrolase from veillonella parvula dsm 2008
3RPC: “The crystal structure of a possible metal-dependent hydrolase from veillonella parvula dsm 2008”. X-ray diffraction, 1 ligand (ZN), 14 pockets (best druggability 0.79). MolNFT v1 #77785 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3RPC
- Type
- protein
- Length
- 1,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Possible metal-dependent hydrolase
- UniProt
- D1BQT4
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Possible metal-dependent hydrolase | protein | 262 | 24% helix, 25% strand | D1BQT4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.79 | 0.82 | 63 | empty |
| 2 | 491 | 0.78 | 0.86 | 61 | empty |
| 3 | 770 | 0.78 | 0.82 | 60 | empty |
| 4 | 478 | 0.78 | 0.86 | 67 | empty |
| 5 | 124 | 0.59 | 0.84 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–C · 984 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 981 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 810 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3RPC · The crystal structure of a possible metal-dependent hydrolase from Veillonella parvula… · 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 D1BQT4
- Elsewhere: RCSB PDB 3RPC · PDBe 3RPC · UniProt D1BQT4
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