MolNFT v1 · #159618 · protein
Cryo-EM structure of bimetallic dodecameric cage design 3 (BMC3) from cytochrome CB562
6OVH · Soluble cytochrome B562: “Cryo-EM structure of bimetallic dodecameric cage design 3 (BMC3) from cytochrome CB562”. Electron microscopy, 4 ligands (HAE, HEC, ZN), 20 pockets (best druggability 0.68). MolNFT v1 #159618 on GenesisL1…
- PDB
- 6OVH
- Type
- protein
- Length
- 1,272 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562
- UniProt
- P0ABE7
- Ligands
- HAE, HEC, ZN, FE
- Pockets
- 20 · best druggability 0.68
Structure
electron microscopy · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Soluble cytochrome B562 | protein | 106 | 75% helix, 0% strand | P0ABE7 |
Ligands and binding sites
- HAE · Acetohydroxamic acid · ligand · 24 copies · chains A, C, F, B, D, I, H, E, G, J, L, K
- HEC · Heme C · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 24 copies · chains A, C, B, F, D, L, G, E, J, H, K, I
- FE · Fe (III) ion · metal · 8 copies · chains A, F, G, B, C, I, D, H, L, E, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.68 | 0.79 | 30 | FE, HAE |
| 2 | 485 | 0.67 | 0.78 | 30 | HAE, FE |
| 3 | 476 | 0.67 | 0.78 | 30 | HAE, FE |
| 4 | 463 | 0.66 | 0.78 | 30 | HAE, FE |
| 5 | 528 | 0.65 | 0.77 | 59 | empty |
Interfaces
30 interfaces between chains.
- F–J · 423 Ų buried · 2 hydrogen bonds · protein-protein
- K–L · 421 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 414 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 2 hydrogen bonds · protein-protein
- B–J · 413 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor, 24 covalent (heme c attachment, covalent ligand).
Compared structures
- 6OVH · Cryo-EM structure of Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562 · the same entry in another collection · chain L against L, 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 P0ABE7
- Elsewhere: RCSB PDB 6OVH · PDBe 6OVH · UniProt P0ABE7
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