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Crystal structure of R153C E. COLI malate dehydrogenase

Analyse Crystal structure of R153C E. COLI malate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IB6
Type: protein
Length: 1,248 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase
EC: 1.1.1.37
UniProt: P61889
Ligands: NAD, SO4
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Malate dehydrogenase (EC 1.1.1.37)	protein	312	46% helix, 17% strand	P61889

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, C, D
SO4 · Sulfate ion · ion · 6 copies · chains A, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	627	0.79	0.84	111	SO4, NAD
2	341	0.71	0.84	72	SO4, NAD
3	229	0.71	0.87	48	SO4, NAD
4	186	0.46	0.75	33	empty
5	166	0.41	0.73	30	empty

Interfaces

5 interfaces between chains.

C–D · 1505 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1494 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 294 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 269 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 170 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1IB6 · Crystal structure of R153C E. COLI malate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
P61889 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P61889) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P61889
Elsewhere: RCSB PDB 1IB6 · PDBe 1IB6 · UniProt P61889

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