MolNFT v1 · #65186 · protein + DNA
Crystal structure of the ternary complex of RECD2 with DNA and adpnp
3GPL · Exodeoxyribonuclease V, subunit recd, putative: “Crystal structure of the ternary complex of RECD2 with DNA and adpnp”. X-ray diffraction, 2 ligands (ANP, MG), 14 pockets (best druggability 0.80). MolNFT v1 #65186 on GenesisL1: 3D…
- PDB
- 3GPL
- Type
- protein + DNA
- Length
- 1,046 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease V, subunit recd, putative; 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3'
- UniProt
- Q9RT63
- Ligands
- ANP, MG
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exodeoxyribonuclease V, subunit recd, putative | protein | 516 | 40% helix, 19% strand | Q9RT63 |
| X, Y | 5'-D(*T*TP*TP*TP*TP*TP*TP*T)-3' | dna | 7 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.80 | 0.87 | 71 | empty |
| 2 | 427 | 0.79 | 0.88 | 67 | empty |
| 3 | 210 | 0.74 | 0.90 | 39 | empty |
| 4 | 207 | 0.72 | 0.88 | 34 | empty |
| 5 | 55 | 0.58 | 0.91 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1551 Ų buried · 12 hydrogen bonds · protein-protein
- A–X · 908 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–Y · 908 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 3GPL · Crystal structure of the ternary complex of RecD2 with DNA and ADPNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RT63 · AlphaFold monomer V2.0 prediction for ATP-dependent recd-like DNA helicase (Q9RT63) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q9RT63
- Elsewhere: RCSB PDB 3GPL · PDBe 3GPL · UniProt Q9RT63
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