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The structure of the mutant, S225A and E251L, of 3-isopropylmalate dehydrogenase from bacillus coagulans

Analyse The structure of the mutant, S225A and E251L, of 3-isopropylmalate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1V5B
Type: protein
Length: 2,853 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: P12010
Ligands: SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	356	42% helix, 22% strand	P12010
B, D, F, G, H	3-isopropylmalate dehydrogenase (EC 1.1.1.85)	protein	357	43% helix, 21% strand	P12010

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, H, 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	973	0.82	0.83	109	SO4
2	158	0.64	0.85	32	empty
3	446	0.63	0.77	31	empty
4	459	0.61	0.76	48	empty
5	434	0.60	0.75	47	empty

Interfaces

8 interfaces between chains.

C–D · 2206 Å² buried · 47 hydrogen bonds · protein-protein
G–H · 2160 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 2141 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 2102 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 654 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1V5B · The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From… · the same entry in another collection · chain G against G, TM-score 1.00
P12010 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (P12010) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P12010
Elsewhere: RCSB PDB 1V5B · PDBe 1V5B · UniProt P12010

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