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The crystal structure of a domain from methanocaldococcus jannaschii dsm 2661
Analyse The crystal structure of a domain from methanocaldococcus jannaschii dsm 2661 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EO4
- Type
- protein
- Length
- 626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ1062
- UniProt
- Q58462
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein MJ1062 | protein | 158 | 31% helix, 34% strand | Q58462 |
| B | Uncharacterized protein MJ1062 | protein | 152 | 34% helix, 32% strand | Q58462 |
| C | Uncharacterized protein MJ1062 | protein | 154 | 34% helix, 34% strand | Q58462 |
| D | Uncharacterized protein MJ1062 | protein | 162 | 32% helix, 35% strand | Q58462 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, D
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.80 | 0.86 | 47 | empty |
| 2 | 504 | 0.77 | 0.84 | 43 | MES |
| 3 | 358 | 0.77 | 0.87 | 41 | MES |
| 4 | 367 | 0.77 | 0.87 | 43 | MES, EDO |
| 5 | 404 | 0.76 | 0.85 | 42 | MES |
Interfaces
4 interfaces between chains.
- C–D · 1051 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1001 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 573 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 572 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3EO4 · The crystal structure of a domain from Methanocaldococcus jannaschii DSM 2661 · the same entry in another collection · chain A against A, TM-score 1.00
- Q58462 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ1062 (Q58462) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q58462
- Elsewhere: RCSB PDB 3EO4 · PDBe 3EO4 · UniProt Q58462
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