Research workbench
Crystal structure of thermotoga maritima mutant D89R/D253R
Analyse Crystal structure of thermotoga maritima mutant D89R/D253R in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JRW
- Type
- protein
- Length
- 1,676 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COBALT/MAGNESIUM transport protein cora
- UniProt
- Q9WZ31
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | COBALT/MAGNESIUM transport protein cora | protein | 333 | 55% helix, 15% strand | Q9WZ31 |
| C | COBALT/MAGNESIUM transport protein cora | protein | 334 | 55% helix, 16% strand | Q9WZ31 |
| D, E | COBALT/MAGNESIUM transport protein cora | protein | 338 | 56% helix, 16% strand | Q9WZ31 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.84 | 0.93 | 48 | MG |
| 2 | 997 | 0.82 | 0.83 | 97 | MG |
| 3 | 800 | 0.74 | 0.79 | 66 | MG |
| 4 | 865 | 0.73 | 0.78 | 71 | MG |
| 5 | 703 | 0.70 | 0.77 | 57 | MG |
Interfaces
10 interfaces between chains.
- D–E · 2666 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 2651 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2519 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2384 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2327 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5JRW · Crystal structure of Thermotoga maritima mutant D89R/D253R · the same entry in another collection · chain E against E, TM-score 1.00
- Q9WZ31 · AlphaFold monomer V2.0 prediction for COBALT/MAGNESIUM transport protein cora (Q9WZ31) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q9WZ31
- Elsewhere: RCSB PDB 5JRW · PDBe 5JRW · UniProt Q9WZ31
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