Research workbench
Structure of the REV1 ctd-REV3/7-pol kappa rir complex
Analyse Structure of the REV1 ctd-REV3/7-pol kappa rir complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FJO
- Type
- protein
- Length
- 347 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein REV1; DNA polymerase kappa; Mitotic spindle assembly checkpoint…
- EC
- 2.7.7.-, 2.7.7.7
- UniProt
- Q920Q2, Q9QUG2, Q9D752, Q61493
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein REV1 (EC 2.7.7.-) | protein | 97 | 71% helix, 4% strand | Q920Q2 |
| B | DNA polymerase kappa | protein | 10 | 60% helix, 0% strand | Q9QUG2 |
| C | Mitotic spindle assembly checkpoint protein MAD2B | protein | 210 | 35% helix, 31% strand | Q9D752 |
| D | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) | protein | 30 | 47% helix, 13% strand | Q61493 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.42 | 0.79 | 17 | PO4 |
| 2 | 93 | 0.40 | 0.77 | 21 | PO4 |
| 3 | 109 | 0.38 | 0.74 | 17 | empty |
| 4 | 67 | 0.34 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1373 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 732 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 510 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4FJO · Structure of the Rev1 CTD-Rev3/7-Pol kappa RIR complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q920Q2 · AlphaFold monomer V2.0 prediction for DNA repair protein REV1 (Q920Q2) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9D752 · AlphaFold monomer V2.0 prediction for mitotic spindle assembly checkpoint protein MAD2B… · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q9QUG2 · AlphaFold monomer V2.0 prediction for DNA polymerase kappa (Q9QUG2) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 Q920Q2
- Every structure of UniProt Q9QUG2
- Every structure of UniProt Q9D752
- Every structure of UniProt Q61493
- Elsewhere: RCSB PDB 4FJO · PDBe 4FJO · UniProt Q920Q2 · UniProt Q9QUG2 · UniProt Q9D752 · UniProt Q61493
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