Research workbench
Semet-labelled hcgc from methanocaldococcus jannaschii in space group P212121
Analyse Semet-labelled hcgc from methanocaldococcus jannaschii in space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D4T
- Type
- protein
- Length
- 1,954 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ0489
- UniProt
- Q57913
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Uncharacterized protein MJ0489 | protein | 243 | 42% helix, 24% strand | Q57913 |
| B | Uncharacterized protein MJ0489 | protein | 246 | 41% helix, 24% strand | Q57913 |
| D, F, G | Uncharacterized protein MJ0489 | protein | 244 | 43% helix, 25% strand | Q57913 |
| H | Uncharacterized protein MJ0489 | protein | 247 | 42% helix, 24% strand | Q57913 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.77 | 0.79 | 55 | empty |
| 2 | 1109 | 0.76 | 0.79 | 57 | empty |
| 3 | 897 | 0.75 | 0.78 | 89 | empty |
| 4 | 431 | 0.75 | 0.84 | 50 | empty |
| 5 | 373 | 0.74 | 0.85 | 52 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1685 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1684 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1674 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1657 Ų buried · 24 hydrogen bonds · protein-protein
- F–H · 649 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- Q57913 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ0489 (Q57913) · 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 Q57913
- Elsewhere: RCSB PDB 5D4T · PDBe 5D4T · UniProt Q57913
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