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Crystal structure of dhydrodipicolinate synthase from acinetobacter baumannii at 2.8A resolution

Analyse Crystal structure of dhydrodipicolinate synthase from acinetobacter baumannii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PUD
Type: protein
Length: 582 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrodipicolinate synthase
EC: 4.2.1.52
UniProt: D0CFC3
Ligands: SO4
Pockets: 3 · best druggability 0.75

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dihydrodipicolinate synthase (EC 4.2.1.52)	protein	291	49% helix, 13% strand	D0CFC3

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 5 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	496	0.75	0.84	65	SO4, GOL
2	92	0.49	0.82	21	empty
3	117	0.49	0.80	20	SO4

Interfaces

1 interface between chains.

A–B · 1485 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3PUD · Crystal structure of Dhydrodipicolinate synthase from Acinetobacter baumannii at 2.8A… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt D0CFC3
Elsewhere: RCSB PDB 3PUD · PDBe 3PUD · UniProt D0CFC3

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