MolNFT v1 · #147387 · protein

Ohrb (organic hydroperoxide resistance protein) mutant (C60A) from chromobacterium violaceum, interacting with dihydrolipoamide

6EBD: “Ohrb (organic hydroperoxide resistance protein) mutant (C60A) from chromobacterium violaceum, interacting…”. X-ray diffraction, 2 ligands (J3S, CL), 5 pockets (best druggability 0.68). MolNFT v1 #147387 on GenesisL1: 3D structure…

PDB: 6EBD
Type: protein
Length: 563 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Organic hydroperoxide resistance protein
UniProt: A0A202B6V5
Ligands: J3S, CL
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Organic hydroperoxide resistance protein	protein	140	33% helix, 31% strand	A0A202B6V5
C	Organic hydroperoxide resistance protein	protein	143	32% helix, 31% strand	A0A202B6V5

Ligands and binding sites

J3S · (6S)-6,8-disulfanyloctanamide · ligand · 3 copies · chains A, B, C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	361	0.68	0.81	39	J3S
2	295	0.67	0.82	31	empty
3	65	0.67	0.95	30	empty
4	411	0.66	0.79	50	J3S
5	296	0.66	0.81	29	J3S

Interfaces

5 interfaces between chains.

C–D · 3180 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 3101 Å² buried · 53 hydrogen bonds · protein-protein
A–C · 207 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 204 Å² buried · 1 hydrogen bond · protein-protein
B–C · 186 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6EBD · OhrB (Organic Hydroperoxide Resistance protein) mutant (C60A) from Chromobacterium… · 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
Every structure of UniProt A0A202B6V5
Elsewhere: RCSB PDB 6EBD · PDBe 6EBD · UniProt A0A202B6V5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.