Research workbench
SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT. Class 2
Analyse SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT. Class 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8EAI
- Type
- protein + DNA
- Length
- 3,017 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.76
- Source
- Saccharolobus solfataricus P2; SYNTHETIC CONSTRUCT
- Molecule
- Minichromosome maintenance protein MCM; 16-mer oligo-dT
- EC
- 3.6.4.12
- UniProt
- Q9UXG1
- Ligands
- 08T, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 2.76 · 4 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Minichromosome maintenance protein MCM (EC 3.6.4.12) | protein | 161 | 6% helix, 42% strand | Q9UXG1 |
| B, C, D, E | Minichromosome maintenance protein MCM (EC 3.6.4.12) | protein | 589 | 38% helix, 24% strand | Q9UXG1 |
| F | Minichromosome maintenance protein MCM (EC 3.6.4.12) | protein | 491 | 32% helix, 25% strand | Q9UXG1 |
| X | 16-mer oligo-dT | dna | 9 | — | — |
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 · 4 copies · chains B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 4 copies · chains 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 | 1153 | 0.86 | 0.87 | 144 | empty |
| 2 | 912 | 0.85 | 0.87 | 120 | MG, 08T |
| 3 | 984 | 0.82 | 0.83 | 104 | MG, 08T |
| 4 | 312 | 0.81 | 0.91 | 51 | MG, 08T |
| 5 | 297 | 0.80 | 0.92 | 49 | MG, 08T |
Interfaces
15 interfaces between chains.
- C–D · 3782 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 3770 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 3735 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 3666 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1725 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 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 0.92
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 Q9UXG1
- Elsewhere: RCSB PDB 8EAI · PDBe 8EAI · UniProt Q9UXG1
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