Research workbench
Crystal structure of the ternary complex of RECD2 with DNA and adpnp
Analyse Crystal structure of the ternary complex of RECD2 with DNA and adpnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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