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Crystal structure of PADHDPS2-H56Q mutant

Analyse Crystal structure of PADHDPS2-H56Q mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P90
Type: protein
Length: 582 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-hydroxy-tetrahydrodipicolinate synthase
EC: 4.3.3.7
UniProt: Q9I4W3
Ligands: CL
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)	protein	291	49% helix, 13% strand	Q9I4W3

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	420	0.76	0.85	50	empty
2	118	0.49	0.80	26	CL
3	114	0.48	0.80	23	CL

Interfaces

1 interface between chains.

A–B · 1576 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

6P90 · Crystal structure of PaDHDPS2-H56Q mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q9I4W3 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q9I4W3) · a predicted model of the same protein · 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 Q9I4W3
Elsewhere: RCSB PDB 6P90 · PDBe 6P90 · UniProt Q9I4W3

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