MolNFT v1 · #147509 · protein

Cryo-EM of the omcs nanowires from geobacter sulfurreducens

6EF8 · C-type cytochrome omcs: “Cryo-EM of the omcs nanowires from geobacter sulfurreducens”. Electron microscopy, 1 ligand (HEC), 16 pockets (best druggability 0.90). MolNFT v1 #147509 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6EF8
Type: protein
Length: 2,849 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-type cytochrome omcs
UniProt: Q74A86
Ligands: HEC
Pockets: 16 · best druggability 0.90

Structure

electron microscopy · 1 distinct chain · 12% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	C-type cytochrome omcs	protein	407	12% helix, 10% strand	Q74A86

Ligands and binding sites

HEC · Heme C · ligand · 42 copies · chains A, B, C, D, E, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	824	0.90	0.93	126	HEC
2	810	0.90	0.93	124	HEC
3	789	0.90	0.93	120	HEC
4	730	0.89	0.93	100	HEC
5	478	0.88	0.95	83	HEC

Interfaces

6 interfaces between chains.

A–B · 1347 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1343 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 1342 Å² buried · 17 hydrogen bonds · protein-protein
C–E · 1340 Å² buried · 17 hydrogen bonds · protein-protein
E–G · 1337 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 77 cofactor (heme c attachment).

Compared structures

6EF8 · Cryo-EM of the OmcS nanowires from Geobacter sulfurreducens · the same entry in another collection · chain G against G, TM-score 1.00
Q74A86 · AlphaFold monomer V2.0 prediction for C-type cytochrome omcs (Q74A86) · a predicted model of the same protein · 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 Q74A86
Elsewhere: RCSB PDB 6EF8 · PDBe 6EF8 · UniProt Q74A86

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