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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: 1PTM
Type: protein
Length: 657 residues
Chains: 2
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, PO4
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4-hydroxythreonine-4-phosphate dehydrogenase (EC 1.1.1.262)	protein	329	40% helix, 18% strand	P19624
B	4-hydroxythreonine-4-phosphate dehydrogenase (EC 1.1.1.262)	protein	328	39% helix, 18% strand	P19624

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · chains A

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

Pockets

6 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	493	0.69	0.80	47	PO4
2	400	0.60	0.76	44	ZN
3	78	0.37	0.77	16	empty
4	62	0.37	0.79	16	empty
5	63	0.36	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 1534 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

1PTM · 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 1PTM · PDBe 1PTM · UniProt P19624

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