MolNFT v1 · #68206 · protein
Structure of the eukaryotic replicative cmg helicase and pumpjack motion
3JC7 · DNA replication licensing factor MCM2: “Structure of the eukaryotic replicative cmg helicase and pumpjack motion”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.88). MolNFT v1 #68206 on GenesisL1: 3D structure…
- PDB
- 3JC7
- Type
- protein
- Length
- 5,075 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication licensing factor MCM2; DNA replication licensing factor MCM3; DNA…
- EC
- 3.6.4.12
- UniProt
- P29469, P24279, P30665, P29496, P53091, P38132, Q08032, Q03406, P40359, Q12488, Q12146
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 11 distinct chains · 38% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 576 | 38% helix, 12% strand | P29469 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 577 | 35% helix, 14% strand | P24279 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 621 | 31% helix, 13% strand | P30665 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 654 | 38% helix, 14% strand | P29496 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 668 | 36% helix, 12% strand | P53091 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 657 | 32% helix, 13% strand | P38132 |
| c | Cell division control protein 45 | protein | 553 | 45% helix, 9% strand | Q08032 |
| D | DNA replication complex gins protein SLD5 | protein | 221 | 50% helix, 3% strand | Q03406 |
| B | DNA replication complex gins protein PSF2 | protein | 181 | 49% helix, 9% strand | P40359 |
| A | DNA replication complex gins protein PSF1 | protein | 208 | 53% helix, 5% strand | Q12488 |
| C | DNA replication complex gins protein PSF3 | protein | 159 | 47% helix, 8% strand | Q12146 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains 7
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 | 1046 | 0.88 | 0.89 | 127 | empty |
| 2 | 1176 | 0.88 | 0.89 | 129 | empty |
| 3 | 825 | 0.87 | 0.90 | 109 | empty |
| 4 | 1125 | 0.86 | 0.87 | 126 | empty |
| 5 | 1119 | 0.84 | 0.85 | 117 | empty |
Interfaces
26 interfaces between chains.
- 3–7 · 4249 Ų buried · 39 hydrogen bonds · protein-protein
- 3–5 · 3986 Ų buried · 52 hydrogen bonds · protein-protein
- 4–7 · 3317 Ų buried · 35 hydrogen bonds · protein-protein
- 2–6 · 2758 Ų buried · 21 hydrogen bonds · protein-protein
- 4–6 · 2647 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3JC7 · Structure of the eukaryotic replicative CMG helicase and pumpjack motion · the same entry in another collection · chain C against C, TM-score 1.00
- Q08032 · AlphaFold monomer V2.0 prediction for cell division control protein 45 (Q08032) · a predicted model of the same protein · chain c against A, TM-score 0.97
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 P29469
- Every structure of UniProt P24279
- Every structure of UniProt P30665
- Every structure of UniProt P29496
- Every structure of UniProt P53091
- Every structure of UniProt P38132
- Every structure of UniProt Q08032
- Every structure of UniProt Q03406
- Every structure of UniProt P40359
- Every structure of UniProt Q12488
- Every structure of UniProt Q12146
- Elsewhere: RCSB PDB 3JC7 · PDBe 3JC7 · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132 · UniProt Q08032 · UniProt Q03406 · UniProt P40359 · UniProt Q12488 · UniProt Q12146
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