MolNFT v1 · #183999 · protein + DNA
Ruva complexed to a holliday junction.
7OA5 · Holliday junction ATP-dependent DNA helicase ruva: “Ruva complexed to a holliday junction.”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.83). MolNFT v1 #183999 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7OA5
- Type
- protein + DNA
- Length
- 1,522 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holliday junction ATP-dependent DNA helicase ruva; DNA…
- EC
- 3.6.4.12
- UniProt
- P40832
- Ligands
- CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 12 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 181 | 46% helix, 23% strand | P40832 |
| B | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 186 | 46% helix, 23% strand | P40832 |
| C | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 184 | 44% helix, 23% strand | P40832 |
| D | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 184 | 48% helix, 23% strand | P40832 |
| E | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 182 | 45% helix, 23% strand | P40832 |
| F | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 184 | 47% helix, 23% strand | P40832 |
| G | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 177 | 46% helix, 24% strand | P40832 |
| H | Holliday junction ATP-dependent DNA helicase ruva (EC 3.6.4.12) | protein | 184 | 46% helix, 23% strand | P40832 |
| I | DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*AP*GP*TP*TP*CP*GP*C)- 3') | dna | 15 | — | — |
| J | DNA (5'-D(*GP*CP*GP*AP*AP*CP*TP*CP*GP*CP*GP*AP*AP*C)-3') | dna | 14 | — | — |
| K | DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)- 3') | dna | 16 | — | — |
| L | DNA (5'-D(P*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)- 3') | dna | 15 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains G, K, A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.83 | 0.96 | 32 | empty |
| 2 | 178 | 0.83 | 0.97 | 32 | empty |
| 3 | 1102 | 0.80 | 0.82 | 121 | CA |
| 4 | 872 | 0.80 | 0.83 | 97 | empty |
| 5 | 764 | 0.78 | 0.83 | 83 | empty |
Interfaces
39 interfaces between chains.
- C–D · 1323 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1306 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1301 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1227 Ų buried · 13 hydrogen bonds · protein-protein
- E–H · 1169 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7OA5 · Ruva complexed to a holliday junction. · the same entry in another collection · chain L against L, 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 P40832
- Elsewhere: RCSB PDB 7OA5 · PDBe 7OA5 · UniProt P40832
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