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Crystal structure of pyrrolo-quinoline quinone (PQQ_DH) from methanococcus maripaludis, northeast structural genomics consortium target MRR86

Analyse Crystal structure of pyrrolo-quinoline quinone (PQQ_DH) from methanococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HXJ
Type: protein
Length: 1,189 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrrolo-quinoline quinone
UniProt: A6VIT4
Ligands: SO4
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyrrolo-quinoline quinone	protein	306	3% helix, 41% strand	A6VIT4
B	Pyrrolo-quinoline quinone	protein	294	1% helix, 40% strand	A6VIT4
C	Pyrrolo-quinoline quinone	protein	286	0% helix, 41% strand	A6VIT4
D	Pyrrolo-quinoline quinone	protein	303	2% helix, 41% strand	A6VIT4

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	856	0.77	0.80	108	empty
2	652	0.71	0.79	69	empty
3	84	0.49	0.82	18	empty
4	110	0.44	0.79	18	empty
5	67	0.44	0.82	19	empty

Interfaces

5 interfaces between chains.

A–D · 1597 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1524 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1380 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 271 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 230 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

3HXJ · Crystal Structure of Pyrrolo-quinoline qui (PQQ_DH) from Methanococcus maripaludis… · 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 A6VIT4
Elsewhere: RCSB PDB 3HXJ · PDBe 3HXJ · UniProt A6VIT4

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