MolNFT v1 · #118820 · protein + DNA
Crystal structure of RECU(D88N) in complex with palindromic DNA duplex
5FDK · Holliday junction resolvase recu: “Crystal structure of RECU(D88N) in complex with palindromic DNA duplex”. X-ray diffraction, 10 pockets (best druggability 0.77). MolNFT v1 #118820 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5FDK
- Type
- protein + DNA
- Length
- 762 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holliday junction resolvase recu; Palindromic DNA
- EC
- 3.1.22.-
- UniProt
- P39792
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holliday junction resolvase recu (EC 3.1.22.-) | protein | 177 | 31% helix, 28% strand | P39792 |
| B | Holliday junction resolvase recu (EC 3.1.22.-) | protein | 166 | 33% helix, 30% strand | P39792 |
| C | Holliday junction resolvase recu (EC 3.1.22.-) | protein | 174 | 29% helix, 26% strand | P39792 |
| D | Holliday junction resolvase recu (EC 3.1.22.-) | protein | 199 | 27% helix, 22% strand | P39792 |
| E, F | Palindromic DNA | dna | 12 | — | — |
| G | Palindromic DNA | dna | 11 | — | — |
| H | Palindromic DNA | dna | 11 | — | — |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.77 | 0.79 | 104 | empty |
| 2 | 311 | 0.72 | 0.85 | 57 | empty |
| 3 | 615 | 0.68 | 0.78 | 60 | empty |
| 4 | 157 | 0.65 | 0.86 | 43 | empty |
| 5 | 132 | 0.54 | 0.82 | 27 | empty |
Interfaces
16 interfaces between chains.
- A–C · 1414 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1265 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 574 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- G–H · 572 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–F · 278 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 5FDK · Crystal structure of RecU(D88N) in complex with palindromic DNA duplex · the same entry in another collection · chain H against H, TM-score 1.00
- P39792 · AlphaFold monomer V2.0 prediction for holliday junction resolvase recu (P39792) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P39792
- Elsewhere: RCSB PDB 5FDK · PDBe 5FDK · UniProt P39792
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