MolNFT v1 · #167190 · protein
Metal-bound C-terminal domain of the czcd transporter from cuprividus metallidurans
6VD9 · Metal cation efflux system protein czcd: “Metal-bound C-terminal domain of the czcd transporter from cuprividus metallidurans”. X-ray diffraction, 1 ligand (NI), 1 pocket (best druggability 0.34). MolNFT v1 #167190 on GenesisL1: 3D…
- PDB
- 6VD9
- Type
- protein
- Length
- 283 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metal cation efflux system protein czcd
- UniProt
- P13512
- Ligands
- NI
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metal cation efflux system protein czcd | protein | 73 | 34% helix, 37% strand | P13512 |
| C | Metal cation efflux system protein czcd | protein | 68 | 37% helix, 37% strand | P13512 |
| D | Metal cation efflux system protein czcd | protein | 69 | 38% helix, 33% strand | P13512 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.34 | 0.78 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 728 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 681 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 304 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 223 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6VD9 · Metal-bound C-terminal domain of the CzcD transporter from Cuprividus metallidurans · the same entry in another collection · chain D against D, TM-score 1.00
- P13512 · AlphaFold monomer V2.0 prediction for metal cation efflux system protein czcd (P13512) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P13512
- Elsewhere: RCSB PDB 6VD9 · PDBe 6VD9 · UniProt P13512
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