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Structure of wrba from yersinia pseudotuberculosis in P1

Analyse Structure of wrba from yersinia pseudotuberculosis in P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q6M
Type: protein
Length: 808 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(P)H dehydrogenase (quinone)
EC: 1.6.5.2
UniProt: Q66BP3
Ligands: CL
Pockets: 9 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2)	protein	198	39% helix, 21% strand	Q66BP3
B, D	NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2)	protein	206	38% helix, 20% strand	Q66BP3

Ligands and binding sites

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

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	145	0.82	0.98	24	empty
2	145	0.80	0.97	34	empty
3	142	0.79	0.96	33	empty
4	450	0.69	0.80	39	CL
5	379	0.68	0.81	39	CL

Interfaces

6 interfaces between chains.

A–D · 1077 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1076 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 890 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 874 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 756 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

7Q6M · Structure of WrbA from Yersinia pseudotuberculosis in P1 · the same entry in another collection · chain A against A, TM-score 1.00
Q66BP3 · AlphaFold monomer V2.0 prediction for NAD(P)H dehydrogenase (quinone) (Q66BP3) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q66BP3
Elsewhere: RCSB PDB 7Q6M · PDBe 7Q6M · UniProt Q66BP3

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