Research workbench
The catalytic core of RAD2 in complex with DNA substrate (complex III)
Analyse The catalytic core of RAD2 in complex with DNA substrate (complex III) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q0Z
- Type
- protein + DNA
- Length
- 1,305 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAD2P; DNA (5'- D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3'); DNA (5'…
- UniProt
- P07276
- Ligands
- CA, K
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAD2P | protein | 322 | 50% helix, 10% strand | P07276 |
| B | RAD2P | protein | 307 | 52% helix, 11% strand | P07276 |
| C | DNA (5'- D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3') | dna | 17 | — | — |
| D, H | DNA (5'- D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3') | dna | 16 | — | — |
| E | RAD2P | protein | 304 | 51% helix, 9% strand | P07276 |
| F | RAD2P | protein | 307 | 54% helix, 8% strand | P07276 |
| G | DNA (5'- D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3') | dna | 16 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, E, F
- K · Potassium ion · metal · 4 copies · chains A, C, B, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.80 | 0.82 | 93 | CA, K |
| 2 | 1194 | 0.78 | 0.80 | 105 | CA, K |
| 3 | 656 | 0.77 | 0.83 | 45 | empty |
| 4 | 1150 | 0.75 | 0.78 | 74 | K |
| 5 | 1109 | 0.74 | 0.77 | 90 | K |
Interfaces
14 interfaces between chains.
- B–F · 748 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 713 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- G–H · 671 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- A–D · 621 Ų buried · 7 hydrogen bonds · protein-nucleic
- F–G · 576 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4Q0Z · The catalytic core of Rad2 in complex with DNA substrate (complex III) · the same entry in another collection · chain H against H, TM-score 1.00
- P07276 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD2 (P07276) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 4Q0Z · PDBe 4Q0Z · UniProt P07276
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