MolNFT v1 · #105544 · protein
Pfmcm-aaa double-octamer
4R7Z · Cell division control protein 21: “Pfmcm-aaa double-octamer”. X-ray diffraction, 2 ligands (ADP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #105544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4R7Z
- Type
- protein
- Length
- 5,056 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division control protein 21
- UniProt
- Q8U3I4
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Cell division control protein 21 | protein | 316 | 43% helix, 9% strand | Q8U3I4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 16 copies · chains A, H, B, C, D, E, F, G, I, P, J, K, L, M, N, O
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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 | 708 | 0.85 | 0.89 | 100 | ADP, MG |
| 2 | 806 | 0.85 | 0.88 | 86 | ADP, MG |
| 3 | 906 | 0.85 | 0.87 | 98 | ADP, MG |
| 4 | 868 | 0.84 | 0.87 | 99 | ADP, MG |
| 5 | 773 | 0.84 | 0.87 | 90 | ADP, MG |
Interfaces
32 interfaces between chains.
- O–P · 1295 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 1252 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 1244 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1231 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 1230 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4R7Z · PfMCM-AAA double-octamer · the same entry in another collection · chain A against A, 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 Q8U3I4
- Elsewhere: RCSB PDB 4R7Z · PDBe 4R7Z · UniProt Q8U3I4
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