MolNFT v1 · #143078 · protein
2.15 ångström resolution crystal structure of malate dehydrogenase from haemophilus influenzae
6AOO: “2.15 ångström resolution crystal structure of malate dehydrogenase from haemophilus influenzae”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.72). MolNFT v1 #143078 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6AOO
- Type
- protein
- Length
- 633 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P44427
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 316 | 48% helix, 17% strand | P44427 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 317 | 48% helix, 17% strand | P44427 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
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 | 580 | 0.72 | 0.80 | 71 | SO4 |
| 2 | 127 | 0.58 | 0.85 | 24 | SO4 |
| 3 | 301 | 0.52 | 0.74 | 41 | empty |
| 4 | 71 | 0.43 | 0.81 | 21 | empty |
| 5 | 99 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1534 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6AOO · 2.15 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus… · the same entry in another collection · chain A against A, TM-score 1.00
- P44427 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P44427) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 6AOO · PDBe 6AOO · UniProt P44427
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