MolNFT v1 · #135765 · protein + DNA
Structure of eukaryotic cmg helicase at a replication fork and implications
5U8T · DNA replication licensing factor MCM2: “Structure of eukaryotic cmg helicase at a replication fork and implications”. Electron microscopy, 1 ligand (ANP), 20 pockets (best druggability 0.87). MolNFT v1 #135765 on GenesisL1: 3D…
- PDB
- 5U8T
- Type
- protein + DNA
- Length
- 5,103 residues
- Chains
- 12
- 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, Q12488, P40359, Q12146, Q03406, Q08032
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 12 distinct chains · 36% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 583 | 36% helix, 13% strand | P29469 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 589 | 33% helix, 15% strand | P24279 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 672 | 30% helix, 13% strand | P30665 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 602 | 36% helix, 16% strand | P29496 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 661 | 32% helix, 8% strand | P53091 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 660 | 29% helix, 12% strand | P38132 |
| A | DNA replication complex gins protein PSF1 | protein | 208 | 51% helix, 3% strand | Q12488 |
| B | DNA replication complex gins protein PSF2 | protein | 181 | 47% helix, 7% strand | P40359 |
| C | DNA replication complex gins protein PSF3 | protein | 159 | 48% helix, 8% strand | Q12146 |
| D | DNA replication complex gins protein SLD5 | protein | 221 | 52% helix, 4% strand | Q03406 |
| E | Cell division control protein 45 | protein | 553 | 44% helix, 9% strand | Q08032 |
| F | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') | dna | 14 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains 2, 6, 3, 5
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 | 1010 | 0.87 | 0.88 | 116 | empty |
| 2 | 824 | 0.86 | 0.89 | 101 | ANP |
| 3 | 1047 | 0.85 | 0.86 | 119 | empty |
| 4 | 984 | 0.85 | 0.86 | 128 | empty |
| 5 | 899 | 0.82 | 0.84 | 112 | empty |
Interfaces
30 interfaces between chains.
- 3–5 · 4495 Ų buried · 30 hydrogen bonds · protein-protein
- 2–6 · 4298 Ų buried · 48 hydrogen bonds · protein-protein
- 4–6 · 3989 Ų buried · 27 hydrogen bonds · protein-protein
- 4–7 · 3782 Ų buried · 34 hydrogen bonds · protein-protein
- 2–5 · 3569 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5U8T · Structure of Eukaryotic CMG Helicase at a Replication Fork and Implications · the same entry in another collection · chain F against F, 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 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 Q12488
- Every structure of UniProt P40359
- Every structure of UniProt Q12146
- Every structure of UniProt Q03406
- Every structure of UniProt Q08032
- Elsewhere: RCSB PDB 5U8T · PDBe 5U8T · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132 · UniProt Q12488 · UniProt P40359 · UniProt Q12146 · UniProt Q03406 · UniProt Q08032
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