Research workbench
Crystal structure of methanocaldococcus jannaschii selecase mutant R36W
Analyse Crystal structure of methanocaldococcus jannaschii selecase mutant R36W in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QHI
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ1213
- UniProt
- Q58610
- Ligands
- ZN, CL
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein MJ1213 | protein | 108 | 54% helix, 13% strand | Q58610 |
| B | Uncharacterized protein MJ1213 | protein | 109 | 49% helix, 13% strand | Q58610 |
| C | Uncharacterized protein MJ1213 | protein | 106 | 58% helix, 13% strand | Q58610 |
| D | Uncharacterized protein MJ1213 | protein | 107 | 53% helix, 13% strand | Q58610 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.54 | 0.75 | 31 | empty |
| 2 | 110 | 0.49 | 0.81 | 22 | empty |
| 3 | 153 | 0.45 | 0.76 | 17 | GOL |
| 4 | 126 | 0.39 | 0.74 | 16 | GOL |
| 5 | 74 | 0.37 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1214 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1154 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4QHI · Crystal structure of Methanocaldococcus jannaschii selecase mutant R36W · the same entry in another collection · chain D against D, TM-score 1.00
- Q58610 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ1213 (Q58610) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q58610
- Elsewhere: RCSB PDB 4QHI · PDBe 4QHI · UniProt Q58610
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