MolNFT v1 · #174066 · protein + DNA
Crystal structure of RECJCDC45 from methanothermobacter thermoautotroficus in complex with ssdna
7BJQ · Conserved protein: “Crystal structure of RECJCDC45 from methanothermobacter thermoautotroficus in complex with ssdna”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.84). MolNFT v1 #174066 on GenesisL1: 3D…
- PDB
- 7BJQ
- Type
- protein + DNA
- Length
- 914 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved protein; DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3')
- UniProt
- O27473
- Ligands
- MN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Conserved protein | protein | 445 | 47% helix, 15% strand | O27473 |
| D, E, F, G | DNA (5'-D(*5P*'P*-P*CP*AP*TP*GP*GP*CP*-P*3P*')-3') | dna | 6 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.85 | 83 | MN |
| 2 | 1076 | 0.81 | 0.82 | 84 | MN |
| 3 | 108 | 0.51 | 0.82 | 17 | empty |
| 4 | 134 | 0.45 | 0.77 | 17 | empty |
Interfaces
11 interfaces between chains.
- B–E · 484 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–G · 454 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–F · 338 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–F · 250 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- B–D · 225 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 7BJQ · Crystal structure of RecJCdc45 from Methanothermobacter thermoautotroficus in complex… · 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 O27473
- Elsewhere: RCSB PDB 7BJQ · PDBe 7BJQ · UniProt O27473
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