MolNFT v1 · #156899 · protein + DNA
Crystal structure of minichromosome maintenance protein MCM/DNA complex
6MII: “Crystal structure of minichromosome maintenance protein MCM/DNA complex”. X-ray diffraction, 4 ligands (08T, ADP, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #156899 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6MII
- Type
- protein + DNA
- Length
- 3,543 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Minichromosome maintenance protein mcm; DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
- EC
- 3.6.4.12
- UniProt
- Q9UXG1
- Ligands
- 08T, ADP, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Minichromosome maintenance protein mcm (EC 3.6.4.12) | protein | 585 | 38% helix, 24% strand | Q9UXG1 |
| B, C, D, F | Minichromosome maintenance protein mcm (EC 3.6.4.12) | protein | 589 | 38% helix, 24% strand | Q9UXG1 |
| E | Minichromosome maintenance protein mcm (EC 3.6.4.12) | protein | 592 | 38% helix, 24% strand | Q9UXG1 |
| X | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- 08T · [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium · ligand · 3 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains D, E, F, A
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 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 | 1158 | 0.85 | 0.86 | 128 | ADP, MG |
| 2 | 671 | 0.84 | 0.89 | 91 | ADP, MG |
| 3 | 363 | 0.81 | 0.90 | 58 | ADP, MG |
| 4 | 254 | 0.80 | 0.93 | 42 | 08T, MG |
| 5 | 510 | 0.80 | 0.86 | 77 | empty |
Interfaces
18 interfaces between chains.
- B–C · 4067 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 4022 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3919 Ų buried · 49 hydrogen bonds · protein-protein
- D–E · 3901 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 3847 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6MII · Crystal structure of minichromosome maintenance protein MCM/DNA complex · the same entry in another collection · chain X against X, TM-score 1.00
- Q9UXG1 · AlphaFold monomer V2.0 prediction for minichromosome maintenance protein mcm (Q9UXG1) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 Q9UXG1
- Elsewhere: RCSB PDB 6MII · PDBe 6MII · UniProt Q9UXG1
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