MolNFT v1 · #128076 · protein

Crystal structure of malate dehydrogenase from plasmodium falciparum (pfmdh)

5NFR: “Crystal structure of malate dehydrogenase from plasmodium falciparum (pfmdh)”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #128076 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NFR
Type: protein
Length: 5,004 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase
EC: 1.1.1.37
UniProt: C6KT25
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, H, I, J, K, L, M, N, O, P	Malate dehydrogenase (EC 1.1.1.37)	protein	313	49% helix, 23% strand	C6KT25
G	Malate dehydrogenase (EC 1.1.1.37)	protein	309	50% helix, 23% strand	C6KT25

Ligands and binding sites

CIT · Citric acid · additive · 15 copies · chains A, B, C, D, E, F, H, I, J, K, L, M, N, O, P

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1118	0.88	0.89	118	empty
2	1174	0.88	0.89	123	empty
3	1154	0.88	0.89	121	empty
4	366	0.83	0.92	51	empty
5	355	0.82	0.92	53	empty

Interfaces

32 interfaces between chains.

A–B · 1913 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1912 Å² buried · 23 hydrogen bonds · protein-protein
K–L · 1911 Å² buried · 22 hydrogen bonds · protein-protein
I–J · 1904 Å² buried · 23 hydrogen bonds · protein-protein
M–N · 1893 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5NFR · Crystal structure of malate dehydrogenase from Plasmodium falciparum (PfMDH) · 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 C6KT25
Elsewhere: RCSB PDB 5NFR · PDBe 5NFR · UniProt C6KT25

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