MolNFT v1 · #148240 · protein
Cryo-EM structure of TRIP13 in complex with ATP gamma S, P31COMET, C- MAD2 and CDC20
6F0X · Pachytene checkpoint protein 2 homolog: “Cryo-EM structure of TRIP13 in complex with ATP gamma S, P31COMET, C- MAD2 and CDC20”. Electron microscopy, 1 ligand (AGS), 20 pockets (best druggability 0.85). MolNFT v1 #148240 on…
- PDB
- 6F0X
- Type
- protein
- Length
- 2,589 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pachytene checkpoint protein 2 homolog; MAD2L1-binding protein; Cell division cycle…
- UniProt
- Q15645, Q15013, Q12834, Q13257
- Ligands
- AGS
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pachytene checkpoint protein 2 homolog | protein | 308 | 47% helix, 9% strand | Q15645 |
| B, C, D, E | Pachytene checkpoint protein 2 homolog | protein | 398 | 47% helix, 13% strand | Q15645 |
| F | Pachytene checkpoint protein 2 homolog | protein | 282 | 49% helix, 9% strand | Q15645 |
| P | MAD2L1-binding protein | protein | 194 | 29% helix, 18% strand | Q15013 |
| Q | Cell division cycle protein 20 homolog | protein | 9 | 0% helix, 22% strand | Q12834 |
| Z | Mitotic spindle assembly checkpoint protein MAD2A | protein | 204 | 31% helix, 27% strand | Q13257 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.85 | 0.86 | 139 | AGS |
| 2 | 818 | 0.81 | 0.84 | 76 | AGS |
| 3 | 1071 | 0.80 | 0.82 | 81 | AGS |
| 4 | 474 | 0.79 | 0.87 | 57 | AGS |
| 5 | 317 | 0.74 | 0.86 | 46 | AGS |
Interfaces
18 interfaces between chains.
- D–E · 2612 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2517 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2517 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2254 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1350 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 6F0X · Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20 · the same entry in another collection · chain Z against Z, TM-score 1.00
- Q15013 · AlphaFold monomer V2.0 prediction for MAD2L1-binding protein (Q15013) · a predicted model of the same protein · chain P against A, TM-score 0.97
- Q15645 · AlphaFold monomer V2.0 prediction for pachytene checkpoint protein 2 homolog (Q15645) · a predicted model of the same protein · chain B against A, TM-score 0.94
- Q13257 · AlphaFold monomer V2.0 prediction for mitotic spindle assembly checkpoint protein MAD2A… · a predicted model of the same protein · chain Z against A, TM-score 0.93
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 Q15645
- Every structure of UniProt Q15013
- Every structure of UniProt Q12834
- Every structure of UniProt Q13257
- Elsewhere: RCSB PDB 6F0X · PDBe 6F0X · UniProt Q15645 · UniProt Q15013 · UniProt Q12834 · UniProt Q13257
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