MolNFT v1 · #171843 · protein
The structure of a cytosolic copper storage protein from methylocystis sp. strain rockwell (atcc 49242)
6ZIF · RKCSP3: “The structure of a cytosolic copper storage protein from methylocystis sp. strain rockwell (atcc 49242)”. X-ray diffraction, 2 ligands (CU1, ZN), 7 pockets (best druggability 0.41). MolNFT v1 #171843 on GenesisL1: 3D…
- PDB
- 6ZIF
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RKCSP3
- Ligands
- CU1, ZN
- Pockets
- 7 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RKCSP3 | protein | 108 | 84% helix, 0% strand | — |
| B, D | RKCSP3 | protein | 107 | 87% helix, 0% strand | — |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 68 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.41 | 0.77 | 15 | empty |
| 2 | 83 | 0.41 | 0.78 | 12 | empty |
| 3 | 118 | 0.40 | 0.75 | 19 | empty |
| 4 | 89 | 0.37 | 0.75 | 12 | empty |
| 5 | 55 | 0.31 | 0.76 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–C · 833 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 830 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 810 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 797 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ZIF · The structure of a cytosolic copper storage protein from Methylocystis sp. Strain… · 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
- Elsewhere: RCSB PDB 6ZIF · PDBe 6ZIF
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