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Ohrb (organic hydroperoxide resistance protein) wild type from chromobacterium violaceum and reduced by dtt

Analyse Ohrb (organic hydroperoxide resistance protein) wild type from chromobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EBC
Type: protein
Length: 565 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Organic hydroperoxide resistance protein
UniProt: A0A202B6V5
Ligands: CL
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Organic hydroperoxide resistance protein	protein	140	33% helix, 32% strand	A0A202B6V5
B	Organic hydroperoxide resistance protein	protein	143	32% helix, 32% strand	A0A202B6V5
D	Organic hydroperoxide resistance protein	protein	142	32% helix, 32% strand	A0A202B6V5

Ligands and binding sites

CL · Chloride ion · ion · 7 copies · chains A, C, B, D
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains B, D, A, C

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	896	0.76	0.80	87	CL
2	252	0.66	0.83	37	empty
3	305	0.65	0.81	44	DTT
4	217	0.65	0.83	30	DTT
5	272	0.64	0.81	36	DTT

Interfaces

6 interfaces between chains.

B–D · 3371 Å² buried · 71 hydrogen bonds · protein-protein
A–C · 3147 Å² buried · 62 hydrogen bonds · protein-protein
A–B · 258 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 112 Å² buried · 1 hydrogen bond · protein-protein
C–D · 79 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6EBC · OhrB (Organic Hydroperoxide Resistance protein) wild type from Chromobacterium violaceum… · 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 6EBC · PDBe 6EBC · UniProt A0A202B6V5

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