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Structure of putative lactate dehydrogenase from francisella tularensis subsp. tularensis schu S4

Analyse Structure of putative lactate dehydrogenase from francisella tularensis subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P7M
Type: protein
Length: 1,273 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase
EC: 1.1.1.37
UniProt: Q8G942
Ligands: PO4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Malate dehydrogenase (EC 1.1.1.37)	protein	318	50% helix, 19% strand	Q8G942
B	Malate dehydrogenase (EC 1.1.1.37)	protein	319	50% helix, 19% strand	Q8G942
D	Malate dehydrogenase (EC 1.1.1.37)	protein	318	50% helix, 19% strand	Q8G942

Ligands and binding sites

PO4 · Phosphate ion · ion · 2 copies · chains C, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	390	0.83	0.91	79	empty
2	394	0.83	0.91	75	empty
3	189	0.77	0.92	27	empty
4	199	0.77	0.92	30	empty
5	496	0.65	0.77	66	empty

Interfaces

6 interfaces between chains.

A–B · 2195 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 2192 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 1049 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 1046 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 696 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 52 modified (engineered).

Compared structures

3P7M · Structure of putative lactate dehydrogenase from Francisella tularensis subsp. tularensis… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8G942
Elsewhere: RCSB PDB 3P7M · PDBe 3P7M · UniProt Q8G942

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