MolNFT v1 · #65385 · protein
Crystal structure of LACTATE/MALATE dehydrogenase from brucella melitensis in complex with ADP
3GVI: “Crystal structure of LACTATE/MALATE dehydrogenase from brucella melitensis in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 18 pockets (best druggability 0.86). MolNFT v1 #65385 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3GVI
- Type
- protein
- Length
- 1,883 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q2YLR9
- Ligands
- ADP
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Malate dehydrogenase (EC 1.1.1.37) | protein | 314 | 52% helix, 20% strand | Q2YLR9 |
| D | Malate dehydrogenase (EC 1.1.1.37) | protein | 313 | 51% helix, 20% strand | Q2YLR9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.86 | 0.88 | 109 | empty |
| 2 | 391 | 0.83 | 0.92 | 55 | empty |
| 3 | 543 | 0.72 | 0.80 | 74 | empty |
| 4 | 516 | 0.70 | 0.80 | 73 | empty |
| 5 | 206 | 0.69 | 0.87 | 33 | empty |
Interfaces
12 interfaces between chains.
- B–C · 2174 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2172 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1274 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1223 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1201 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3GVI · Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex… · the same entry in another collection · chain F against F, TM-score 1.00
- Q2YLR9 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q2YLR9) · 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 Q2YLR9
- Elsewhere: RCSB PDB 3GVI · PDBe 3GVI · UniProt Q2YLR9
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