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Crystal structure of putative 3-isopropylmalate dehydrogenase from campylobacter jejuni

Analyse Crystal structure of putative 3-isopropylmalate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3UDU
Type: protein
Length: 2,839 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-isopropylmalate dehydrogenase
EC: 1.1.1.85
UniProt: Q9PLW0
Ligands: CL
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F, G	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	356	49% helix, 21% strand	Q9PLW0
B, E	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	355	49% helix, 20% strand	Q9PLW0
C	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	351	48% helix, 21% strand	Q9PLW0
H	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	354	50% helix, 18% strand	Q9PLW0

Ligands and binding sites

CL · Chloride ion · ion · chains C
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, E, D, F, G

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1114	0.77	0.79	124	EDO
2	498	0.73	0.82	56	empty
3	502	0.72	0.81	68	empty
4	129	0.67	0.89	26	empty
5	135	0.64	0.87	25	empty

Interfaces

15 interfaces between chains.

A–B · 2076 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2045 Å² buried · 36 hydrogen bonds · protein-protein
F–H · 543 Å² buried · 9 hydrogen bonds · protein-protein
E–G · 502 Å² buried · 8 hydrogen bonds · protein-protein
C–G · 382 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3UDU · Crystal structure of putative 3-isopropylmalate dehydrogenase from Campylobacter jejuni · the same entry in another collection · chain H against H, TM-score 1.00
Q9PLW0 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (Q9PLW0) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9PLW0
Elsewhere: RCSB PDB 3UDU · PDBe 3UDU · UniProt Q9PLW0

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