Research workbench
1.7 a resolution structure of wild type malate dehydrogenase from haloarcula marismortui
Analyse 1.7 a resolution structure of wild type malate dehydrogenase from haloarcula… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JCO
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q07841
- Ligands
- NA, CL
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 50% helix, 20% strand | Q07841 |
Ligands and binding sites
- NA · Sodium ion · metal · 26 copies · chains A, C, B, D
- CL · Chloride ion · ion · 13 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.81 | 0.83 | 141 | NA |
| 2 | 701 | 0.79 | 0.83 | 60 | empty |
| 3 | 556 | 0.67 | 0.77 | 55 | CL, NA |
| 4 | 520 | 0.66 | 0.77 | 51 | CL, NA |
| 5 | 500 | 0.65 | 0.77 | 52 | CL |
Interfaces
6 interfaces between chains.
- A–B · 2199 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2166 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 743 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4JCO · 1.7 A resolution structure of wild type malate dehydrogenase from haloarcula marismortui · the same entry in another collection · chain A against A, TM-score 1.00
- Q07841 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q07841) · a predicted model of the same protein · 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 Q07841
- Elsewhere: RCSB PDB 4JCO · PDBe 4JCO · UniProt Q07841
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