Research workbench
Crystal structure of putative DNA binding protein from methanocaldococcus jannaschii.
Analyse Crystal structure of putative DNA binding protein from methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LHK
- Type
- protein
- Length
- 581 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative DNA binding protein MJ0014
- UniProt
- Q60329
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative DNA binding protein MJ0014 | protein | 146 | 54% helix, 16% strand | Q60329 |
| B, D | Putative DNA binding protein MJ0014 | protein | 145 | 54% helix, 15% strand | Q60329 |
| C | Putative DNA binding protein MJ0014 | protein | 145 | 54% helix, 17% strand | Q60329 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.65 | 0.78 | 59 | empty |
| 2 | 417 | 0.64 | 0.78 | 51 | empty |
| 3 | 253 | 0.54 | 0.76 | 36 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1781 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1768 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 299 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 282 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3LHK · Crystal structure of putative DNA binding protein from Methanocaldococcus jannaschii. · the same entry in another collection · chain A against A, TM-score 1.00
- Q60329 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ0014 (Q60329) · a predicted model of the same protein · chain B 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 Q60329
- Elsewhere: RCSB PDB 3LHK · PDBe 3LHK · UniProt Q60329
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