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Crystal structure of malate dehydrogenase from thermus thermophilus HB8

Analyse Crystal structure of malate dehydrogenase from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IZ9
Type: protein
Length: 654 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase
EC: 1.1.1.37
UniProt: P10584
Pockets: 7 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Malate dehydrogenase (EC 1.1.1.37)	protein	327	46% helix, 19% strand	P10584

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	427	0.60	0.76	54	empty
2	374	0.58	0.75	50	empty
3	222	0.52	0.77	34	empty
4	209	0.52	0.77	34	empty
5	140	0.49	0.79	20	empty

Interfaces

1 interface between chains.

A–B · 1677 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

1IZ9 · Crystal Structure of Malate Dehydrogenase from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
P10584 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P10584) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P10584
Elsewhere: RCSB PDB 1IZ9 · PDBe 1IZ9 · UniProt P10584

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