MolNFT v1 · #98560 · protein + DNA
T. thermophilus ruvc in complex with holliday junction substrate
4LD0 · Crossover junction endodeoxyribonuclease ruvc: “T. thermophilus ruvc in complex with holliday junction substrate”. X-ray diffraction, 7 pockets (best druggability 0.78). MolNFT v1 #98560 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4LD0
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crossover junction endodeoxyribonuclease ruvc; DNA 31-mer; DNA 13-mer; DNA 11-mer
- EC
- 3.1.22.4
- UniProt
- Q5SJC4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Crossover junction endodeoxyribonuclease ruvc (EC 3.1.22.4) | protein | 158 | 48% helix, 22% strand | Q5SJC4 |
| B | Crossover junction endodeoxyribonuclease ruvc (EC 3.1.22.4) | protein | 157 | 49% helix, 20% strand | Q5SJC4 |
| C | DNA 31-mer | dna | 31 | — | — |
| D | DNA 13-mer | dna | 13 | — | — |
| F | DNA 11-mer | dna | 11 | — | — |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.78 | 0.81 | 91 | empty |
| 2 | 609 | 0.73 | 0.80 | 50 | empty |
| 3 | 59 | 0.69 | 0.96 | 24 | empty |
| 4 | 580 | 0.66 | 0.76 | 41 | empty |
| 5 | 87 | 0.58 | 0.87 | 25 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1022 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 576 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 464 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–F · 376 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- C–D · 355 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Compared structures
- 4LD0 · T. thermophilus RuvC in complex with Holliday junction substrate · the same entry in another collection · chain B against B, TM-score 1.00
- Q5SJC4 · AlphaFold monomer V2.0 prediction for crossover junction endodeoxyribonuclease ruvc… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q5SJC4
- Elsewhere: RCSB PDB 4LD0 · PDBe 4LD0 · UniProt Q5SJC4
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