Research workbench
He catalytic core of RAD2 in complex with DNA substrate (complex II)
Analyse He catalytic core of RAD2 in complex with DNA substrate (complex II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q0W
- Type
- protein + DNA
- Length
- 647 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD2; DNA (5'- D(*TP*TP*TP*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)…
- EC
- 3.1.-.-
- UniProt
- P07276
- Ligands
- CA, K
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD2 (EC 3.1.-.-) | protein | 316 | 54% helix, 11% strand | P07276 |
| B | DNA repair protein RAD2 (EC 3.1.-.-) | protein | 301 | 51% helix, 10% strand | P07276 |
| C | DNA (5'- D(*TP*TP*TP*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)-3') | dna | 15 | — | — |
| D | DNA (5'- D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3') | dna | 15 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.75 | 0.81 | 53 | empty |
| 2 | 746 | 0.74 | 0.79 | 52 | K |
| 3 | 367 | 0.69 | 0.82 | 43 | empty |
| 4 | 371 | 0.69 | 0.82 | 48 | empty |
| 5 | 528 | 0.65 | 0.77 | 35 | K |
Interfaces
6 interfaces between chains.
- C–D · 659 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- A–C · 507 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 472 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 403 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 277 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 4Q0W · he catalytic core of Rad2 in complex with DNA substrate (complex II) · the same entry in another collection · chain A against A, TM-score 1.00
- P07276 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD2 (P07276) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P07276
- Elsewhere: RCSB PDB 4Q0W · PDBe 4Q0W · UniProt P07276
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