MolNFT v1 · #159547 · protein
Bimetallic dodecameric cage design 2 (BMC2) from cytochrome CB562
6OT4 · Soluble cytochrome B562: “Bimetallic dodecameric cage design 2 (BMC2) from cytochrome CB562”. X-ray diffraction, 4 ligands (HAE, HEC, ZN), 7 pockets (best druggability 0.71). MolNFT v1 #159547 on GenesisL1: 3D structure, binding…
- PDB
- 6OT4
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HAE, HEC, ZN, FE
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Soluble cytochrome B562 | protein | 106 | 80% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HAE · Acetohydroxamic acid · ligand · 8 copies · chains A, D, B, C
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, C, B, D
- FE · Fe (III) ion · metal · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.71 | 0.78 | 73 | empty |
| 2 | 526 | 0.67 | 0.77 | 50 | empty |
| 3 | 408 | 0.66 | 0.79 | 57 | HEC |
| 4 | 160 | 0.61 | 0.83 | 25 | HEC |
| 5 | 152 | 0.58 | 0.82 | 25 | HEC |
Interfaces
5 interfaces between chains.
- C–D · 459 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 422 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 403 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 267 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 148 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 8 covalent (heme c attachment, covalent ligand).
Compared structures
- 6OT4 · Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562 · the same entry in another collection · chain D against D, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P0ABE7
- Elsewhere: RCSB PDB 6OT4 · PDBe 6OT4 · UniProt P0ABE7
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