MolNFT v1 · #92816 · protein
Crystal structure of human REV3-REV7-REV1-polkappa complex
4GK5 · Mitotic spindle assembly checkpoint protein MAD2B: “Crystal structure of human REV3-REV7-REV1-polkappa complex”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1 #92816 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4GK5
- Type
- protein
- Length
- 625 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitotic spindle assembly checkpoint protein MAD2B; DNA polymerase zeta catalytic subunit…
- EC
- 2.7.7.7, 2.7.7.-
- UniProt
- Q9UI95, O60673, Q9UBZ9, Q9UBT6
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitotic spindle assembly checkpoint protein MAD2B | protein | 198 | 38% helix, 31% strand | Q9UI95 |
| B | Mitotic spindle assembly checkpoint protein MAD2B | protein | 190 | 38% helix, 29% strand | Q9UI95 |
| C, D | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) | protein | 20 | 20% helix, 20% strand | O60673 |
| E | DNA repair protein REV1 (EC 2.7.7.-) | protein | 96 | 71% helix, 4% strand | Q9UBZ9 |
| F | DNA repair protein REV1 (EC 2.7.7.-) | protein | 93 | 68% helix, 4% strand | Q9UBZ9 |
| G | DNA polymerase kappa (EC 2.7.7.7) | protein | 8 | 0% helix, 0% strand | Q9UBT6 |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.71 | 0.77 | 61 | empty |
| 2 | 71 | 0.41 | 0.79 | 12 | empty |
| 3 | 91 | 0.40 | 0.77 | 18 | empty |
| 4 | 70 | 0.39 | 0.79 | 18 | empty |
| 5 | 108 | 0.38 | 0.75 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1208 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1195 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 738 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 698 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 626 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4GK5 · Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q9UI95 · AlphaFold monomer V2.0 prediction for mitotic spindle assembly checkpoint protein MAD2B… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9UBZ9 · AlphaFold monomer V2.0 prediction for DNA repair protein REV1 (Q9UBZ9) · a predicted model of the same protein · chain E against A, TM-score 0.97
- Q9UBT6 · AlphaFold monomer V2.0 prediction for DNA polymerase kappa (Q9UBT6) · a predicted model of the same protein · chain G against A, TM-score 0.57
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 Q9UI95
- Every structure of UniProt O60673
- Every structure of UniProt Q9UBZ9
- Every structure of UniProt Q9UBT6
- Elsewhere: RCSB PDB 4GK5 · PDBe 4GK5 · UniProt Q9UI95 · UniProt O60673 · UniProt Q9UBZ9 · UniProt Q9UBT6
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