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Structure of pdxj

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

PDB: 6RG0
Type: protein
Length: 946 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxine 5'-phosphate synthase
EC: 2.6.99.2
UniProt: P0A794
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Pyridoxine 5'-phosphate synthase (EC 2.6.99.2)	protein	242	50% helix, 18% strand	P0A794
D	Pyridoxine 5'-phosphate synthase (EC 2.6.99.2)	protein	220	40% helix, 19% strand	P0A794

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.77	0.79	85	empty
2	838	0.74	0.78	74	empty
3	300	0.62	0.80	37	empty
4	179	0.51	0.78	20	empty
5	185	0.49	0.77	26	empty

Interfaces

5 interfaces between chains.

A–B · 1143 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 725 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 547 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 343 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 307 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6RG0 · Structure of pdxj · the same entry in another collection · chain A against A, TM-score 1.00
P0A794 · AlphaFold monomer V2.0 prediction for pyridoxine 5'-phosphate synthase (P0A794) · 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 P0A794
Elsewhere: RCSB PDB 6RG0 · PDBe 6RG0 · UniProt P0A794

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