MolNFT v1 · #125000 · protein
Structure of malate dehydrogenase in complex with NADH from mycobacterium tuberculosis
5KVV: “Structure of malate dehydrogenase in complex with NADH from mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (NAI, SO4), 6 pockets (best druggability 0.71). MolNFT v1 #125000 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5KVV
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P9WK13
- Ligands
- NAI, SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 327 | 47% helix, 19% strand | P9WK13 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 326 | 47% helix, 19% strand | P9WK13 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.71 | 0.82 | 53 | NAI, SO4 |
| 2 | 431 | 0.71 | 0.82 | 45 | NAI, TRS |
| 3 | 606 | 0.70 | 0.79 | 68 | empty |
| 4 | 97 | 0.39 | 0.77 | 17 | empty |
| 5 | 110 | 0.38 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1453 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5KVV · Structure of Malate Dehydrogenase in complex with NADH from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- P9WK13 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P9WK13) · a predicted model of the same protein · chain B 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 P9WK13
- Elsewhere: RCSB PDB 5KVV · PDBe 5KVV · UniProt P9WK13
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