MolNFT v1 · #51723 · protein
Structure of the symmetric MAD2 dimer
2VFX · Mitotic spindle assembly checkpoint protein MAD2A: “Structure of the symmetric MAD2 dimer”. X-ray diffraction, 2 ligands (MG, CL), 20 pockets (best druggability 0.80). MolNFT v1 #51723 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VFX
- Type
- protein
- Length
- 2,438 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitotic spindle assembly checkpoint protein MAD2A
- UniProt
- Q13257
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, H | Mitotic spindle assembly checkpoint protein MAD2A | protein | 203 | 31% helix, 33% strand | Q13257 |
| D, I | Mitotic spindle assembly checkpoint protein MAD2A | protein | 202 | 31% helix, 30% strand | Q13257 |
| E, K | Mitotic spindle assembly checkpoint protein MAD2A | protein | 206 | 32% helix, 31% strand | Q13257 |
| G, L | Mitotic spindle assembly checkpoint protein MAD2A | protein | 203 | 32% helix, 30% strand | Q13257 |
| J | Mitotic spindle assembly checkpoint protein MAD2A | protein | 201 | 31% helix, 30% strand | Q13257 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, E, F, G, K, L
- CL · Chloride ion · ion · 37 copies · chains A, B, E, C, D, G, H, F, I, L, J, K
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 6 copies · chains B, C, F, G, K
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 3 copies · chains A, B, E, I, L
- PEG · Di(hydroxyethyl)ether · additive · chains I
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 | 787 | 0.80 | 0.84 | 71 | empty |
| 2 | 781 | 0.79 | 0.83 | 83 | empty |
| 3 | 676 | 0.67 | 0.76 | 63 | CL, PEG, PE4 |
| 4 | 598 | 0.66 | 0.76 | 45 | CL, PE3 |
| 5 | 651 | 0.65 | 0.75 | 59 | CL, PE3, PE4 |
Interfaces
20 interfaces between chains.
- A–E · 966 Ų buried · 16 hydrogen bonds · protein-protein
- F–I · 962 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 949 Ų buried · 15 hydrogen bonds · protein-protein
- C–J · 917 Ų buried · 14 hydrogen bonds · protein-protein
- C–I · 510 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VFX · Structure of the Symmetric Mad2 Dimer · the same entry in another collection · chain L against L, TM-score 1.00
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 2VFX · PDBe 2VFX · UniProt Q13257
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