MolNFT v2 · #120172 · protein
DNA replication protein
5GHS · SsDNA-specific exonuclease: “DNA replication protein”. X-ray diffraction at 2.591, 1 ligand (SO4), 14 pockets (best druggability 0.52). MolNFT v2 #120172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GHS
- Type
- protein
- Length
- 922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.591
- Source
- Thermococcus kodakarensis; Thermococcus kodakarensis (strain ATCC BAA-918 / JCM…
- Molecule
- SsDNA-specific exonuclease; Putative uncharacterized protein
- UniProt
- Q5JGL0, Q5JF31
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.52
Structure
x-ray diffraction · resolution 2.591 · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SsDNA-specific exonuclease | protein | 450 | 51% helix, 14% strand | Q5JGL0 |
| B | SsDNA-specific exonuclease | protein | 345 | 54% helix, 12% strand | Q5JGL0 |
| C | Putative uncharacterized protein | protein | 56 | 16% helix, 38% strand | Q5JF31 |
| D | Putative uncharacterized protein | protein | 71 | 11% helix, 30% strand | Q5JF31 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.52 | 0.74 | 35 | empty |
| 2 | 172 | 0.46 | 0.75 | 33 | empty |
| 3 | 98 | 0.43 | 0.78 | 15 | empty |
| 4 | 74 | 0.41 | 0.79 | 13 | empty |
| 5 | 117 | 0.40 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 937 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 869 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 263 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5GHS · DNA replication protein · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5JGL0
- Every structure of UniProt Q5JF31
- Elsewhere: RCSB PDB 5GHS · PDBe 5GHS · UniProt Q5JGL0 · UniProt Q5JF31
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