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Crystal structure of E.COLI pdxa

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

PDB: 1PS7
Type: protein
Length: 1,312 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-hydroxythreonine-4-phosphate dehydrogenase
EC: 1.1.1.262
UniProt: P19624
Ligands: ZN
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	4-hydroxythreonine-4-phosphate dehydrogenase (EC 1.1.1.262)	protein	328	41% helix, 16% strand	P19624

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D

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

Pockets

7 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	540	0.70	0.80	55	ZN
2	520	0.70	0.80	52	empty
3	443	0.62	0.76	50	ZN
4	434	0.60	0.75	57	ZN
5	96	0.41	0.77	22	empty

Interfaces

3 interfaces between chains.

A–B · 1529 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1528 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 158 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 modified (engineered).

Compared structures

1PS7 · Crystal structure of E.coli PdxA · the same entry in another collection · chain A against A, TM-score 1.00
P19624 · AlphaFold monomer V2.0 prediction for 4-hydroxythreonine-4-phosphate dehydrogenase… · 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 P19624
Elsewhere: RCSB PDB 1PS7 · PDBe 1PS7 · UniProt P19624

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