MolNFT v1 · #104112 · protein + DNA
He catalytic core of RAD2 in complex with DNA substrate (complex II)
4Q0W · DNA repair protein RAD2: “He catalytic core of RAD2 in complex with DNA substrate (complex II)”. X-ray diffraction, 2 ligands (CA, K), 8 pockets (best druggability 0.75). MolNFT v1 #104112 on GenesisL1: 3D structure, binding sites…
- 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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