Research workbench
2.25 a resolution structure of the wild type malate dehydrogenase from haloarcula marismortui after second radiation burn (radiation damage series)
Analyse 2.25 a resolution structure of the wild type malate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J5R
- Type
- protein
- Length
- 1,202 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
- CL
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Malate dehydrogenase (EC 1.1.1.37) | protein | 303 | 50% helix, 20% strand | Q07841 |
| B, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 298 | 49% helix, 21% strand | Q07841 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.79 | 0.84 | 63 | empty |
| 2 | 633 | 0.79 | 0.84 | 51 | empty |
| 3 | 508 | 0.64 | 0.76 | 51 | empty |
| 4 | 459 | 0.63 | 0.76 | 48 | empty |
| 5 | 372 | 0.59 | 0.76 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2250 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2208 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 717 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 694 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 162 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2J5R · 2.25 A resolution structure of the wild type malate dehydrogenase from Haloarcula… · 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 B 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 2J5R · PDBe 2J5R · UniProt Q07841
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