MolNFT v1 · #143812 · protein
2.1 ångström resolution crystal structure of malate dehydrogenase from haemophilus influenzae in complex with L-malate
6BAL: “2.1 ångström resolution crystal structure of malate dehydrogenase from haemophilus influenzae in complex with…”. X-ray diffraction, 2 ligands (LMR, CL), 20 pockets (best druggability 0.90). MolNFT v1 #143812 on GenesisL1: 3D…
- PDB
- 6BAL
- Type
- protein
- Length
- 2,491 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P44427
- Ligands
- LMR, CL
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Malate dehydrogenase (EC 1.1.1.37) | protein | 312 | 47% helix, 17% strand | P44427 |
| B, C, H | Malate dehydrogenase (EC 1.1.1.37) | protein | 313 | 50% helix, 17% strand | P44427 |
| F | Malate dehydrogenase (EC 1.1.1.37) | protein | 314 | 47% helix, 17% strand | P44427 |
| G | Malate dehydrogenase (EC 1.1.1.37) | protein | 302 | 48% helix, 18% strand | P44427 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · chains A
- CL · Chloride ion · ion · 17 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.90 | 0.92 | 175 | CL |
| 2 | 974 | 0.86 | 0.87 | 144 | LMR |
| 3 | 909 | 0.81 | 0.84 | 109 | empty |
| 4 | 119 | 0.69 | 0.91 | 29 | empty |
| 5 | 315 | 0.56 | 0.76 | 47 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1575 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1550 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1538 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1536 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 1069 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6BAL · 2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus… · the same entry in another collection · chain H against H, TM-score 1.00
- P44427 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P44427) · a predicted model of the same protein · chain G 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 P44427
- Elsewhere: RCSB PDB 6BAL · PDBe 6BAL · UniProt P44427
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