Research workbench
Hcgc from methanocaldococcus jannaschii
Analyse Hcgc from methanocaldococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D5O
- Type
- protein
- Length
- 1,966 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ0489
- UniProt
- Q57913
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein MJ0489 | protein | 246 | 43% helix, 25% strand | Q57913 |
| B | Uncharacterized protein MJ0489 | protein | 244 | 41% helix, 23% strand | Q57913 |
| C, G | Uncharacterized protein MJ0489 | protein | 245 | 43% helix, 26% strand | Q57913 |
| D, H | Uncharacterized protein MJ0489 | protein | 248 | 42% helix, 26% strand | Q57913 |
| E | Uncharacterized protein MJ0489 | protein | 247 | 43% helix, 26% strand | Q57913 |
| F | Uncharacterized protein MJ0489 | protein | 243 | 43% helix, 23% strand | Q57913 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.76 | 0.82 | 80 | empty |
| 2 | 1020 | 0.76 | 0.79 | 55 | empty |
| 3 | 1069 | 0.76 | 0.79 | 63 | empty |
| 4 | 326 | 0.76 | 0.87 | 41 | empty |
| 5 | 880 | 0.76 | 0.79 | 89 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1697 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1695 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1693 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1657 Ų buried · 23 hydrogen bonds · protein-protein
- E–H · 644 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- Q57913 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ0489 (Q57913) · a predicted model of the same protein · chain A 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 Q57913
- Elsewhere: RCSB PDB 5D5O · PDBe 5D5O · UniProt Q57913
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