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Crystallographic structure of the conformational dimer of the spindle assembly checkpoint protein MAD2.
Analyse Crystallographic structure of the conformational dimer of the spindle assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V64
- Type
- protein
- Length
- 1,187 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitotic spindle assembly checkpoint protein MAD2A; MBP1
- UniProt
- Q13257
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Mitotic spindle assembly checkpoint protein MAD2A | protein | 210 | 36% helix, 32% strand | Q13257 |
| B, G | MBP1 | protein | 10 | 0% helix, 30% strand | — |
| D | Mitotic spindle assembly checkpoint protein MAD2A | protein | 171 | 34% helix, 35% strand | Q13257 |
| E | Mitotic spindle assembly checkpoint protein MAD2A | protein | 175 | 33% helix, 33% strand | Q13257 |
| H | Mitotic spindle assembly checkpoint protein MAD2A | protein | 180 | 32% helix, 33% strand | Q13257 |
| I | MBP1 | protein | 11 | 0% helix, 36% strand | — |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.73 | 0.81 | 54 | empty |
| 2 | 609 | 0.73 | 0.81 | 68 | empty |
| 3 | 506 | 0.72 | 0.81 | 50 | empty |
| 4 | 251 | 0.61 | 0.80 | 33 | empty |
| 5 | 161 | 0.55 | 0.80 | 19 | empty |
Interfaces
15 interfaces between chains.
- A–E · 1049 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 1028 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1009 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 982 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 972 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2V64 · Crystallographic structure of the conformational dimer of the Spindle Assembly Checkpoint… · the same entry in another collection · chain I against I, TM-score 1.00
- 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 0.92
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
- Elsewhere: RCSB PDB 2V64 · PDBe 2V64 · UniProt Q13257
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