Research workbench
Crystal structure of methanosarcina acetivorans methanoredoxin
Analyse Crystal structure of methanosarcina acetivorans methanoredoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CAX
- Type
- protein
- Length
- 382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaredoxin
- UniProt
- Q8TQ93
- Ligands
- CD, SO4
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glutaredoxin | protein | 96 | 40% helix, 18% strand | Q8TQ93 |
| B | Glutaredoxin | protein | 95 | 40% helix, 22% strand | Q8TQ93 |
| C | Glutaredoxin | protein | 95 | 40% helix, 23% strand | Q8TQ93 |
Ligands and binding sites
- CD · Cadmium ion · metal · 12 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- ACY · Acetic acid · additive · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.84 | 0.85 | 100 | CD, ACY |
| 2 | 99 | 0.62 | 0.88 | 19 | empty |
| 3 | 52 | 0.24 | 0.72 | 10 | empty |
Interfaces
5 interfaces between chains.
- B–C · 647 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 455 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 45 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5CAX · Crystal structure of methanosarcina acetivorans methanoredoxin · the same entry in another collection · 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 Q8TQ93
- Elsewhere: RCSB PDB 5CAX · PDBe 5CAX · UniProt Q8TQ93
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