MolNFT v1 · #160134 · protein

Crystal structure of malate dehydrogenase from legionella pneumophila philadelphia 1

6PBL: “Crystal structure of malate dehydrogenase from legionella pneumophila philadelphia 1”. X-ray diffraction, 9 pockets (best druggability 0.69). MolNFT v1 #160134 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PBL
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: Q5ZT13
Pockets: 9 · best druggability 0.69

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	Q5ZT13

Pockets

9 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	702	0.69	0.77	58	empty
2	386	0.61	0.77	38	empty
3	432	0.60	0.76	51	empty
4	136	0.58	0.84	26	empty
5	103	0.49	0.81	15	empty

Interfaces

1 interface between chains.

A–B · 1656 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

6PBL · Crystal structure of Malate dehydrogenase from Legionella pneumophila Philadelphia 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q5ZT13 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q5ZT13) · 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 Q5ZT13
Elsewhere: RCSB PDB 6PBL · PDBe 6PBL · UniProt Q5ZT13

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