Research workbench
Crystal structure of the MAD2/P31(COMET)/MAD2-binding peptide ternary complex
Analyse Crystal structure of the MAD2/P31(COMET)/MAD2-binding peptide ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QYF
- Type
- protein
- Length
- 780 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitotic spindle assembly checkpoint protein MAD2A; MAD2L1-binding protein; Peptide
- UniProt
- Q13257, Q15013
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitotic spindle assembly checkpoint protein MAD2A | protein | 197 | 36% helix, 31% strand | Q13257 |
| B | MAD2L1-binding protein | protein | 188 | 29% helix, 23% strand | Q15013 |
| C | Mitotic spindle assembly checkpoint protein MAD2A | protein | 183 | 35% helix, 32% strand | Q13257 |
| D | MAD2L1-binding protein | protein | 191 | 34% helix, 23% strand | Q15013 |
| E | Peptide | protein | 11 | 0% helix, 36% strand | — |
| F | Peptide | protein | 10 | 0% helix, 40% strand | — |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.75 | 0.88 | 44 | empty |
| 2 | 619 | 0.72 | 0.79 | 63 | empty |
| 3 | 278 | 0.59 | 0.78 | 28 | empty |
| 4 | 246 | 0.57 | 0.78 | 27 | empty |
| 5 | 51 | 0.54 | 0.89 | 14 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1177 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1175 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 966 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 958 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 2QYF · Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q15013 · AlphaFold monomer V2.0 prediction for MAD2L1-binding protein (Q15013) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q13257 · AlphaFold monomer V2.0 prediction for mitotic spindle assembly checkpoint protein MAD2A… · a predicted model of the same protein · chain A 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 Q13257
- Every structure of UniProt Q15013
- Elsewhere: RCSB PDB 2QYF · PDBe 2QYF · UniProt Q13257 · UniProt Q15013
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