MolNFT v1 · #135764 · protein + DNA
Structure of eukaryotic cmg helicase at a replication fork
5U8S · DNA replication complex gins protein PSF1: “Structure of eukaryotic cmg helicase at a replication fork”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.88). MolNFT v1 #135764 on GenesisL1: 3D structure, binding…
- PDB
- 5U8S
- Type
- protein + DNA
- Length
- 5,101 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication complex gins protein PSF1; DNA replication complex gins protein PSF2; DNA…
- EC
- 3.6.4.12
- UniProt
- Q12488, P40359, Q12146, Q03406, Q08032, P29469, P24279, P30665, P29496, P53091, P38132
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 13 distinct chains · 38% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA replication complex gins protein PSF1 | protein | 208 | 53% helix, 4% strand | Q12488 |
| B | DNA replication complex gins protein PSF2 | protein | 181 | 48% helix, 7% strand | P40359 |
| C | DNA replication complex gins protein PSF3 | protein | 159 | 54% helix, 6% strand | Q12146 |
| D | DNA replication complex gins protein SLD5 | protein | 221 | 49% helix, 4% strand | Q03406 |
| E | Cell division control protein 45 | protein | 553 | 46% helix, 7% strand | Q08032 |
| F | DNA (26-mer) | dna | 26 | — | — |
| G | DNA (5'-D(P*AP*TP*CP*GP*AP*TP*CP*GP*AP*TP*CP*GP*AP*T)-3') | dna | 14 | — | — |
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 602 | 38% helix, 13% strand | P29469 |
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 591 | 35% helix, 15% strand | P24279 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 682 | 35% helix, 12% strand | P30665 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 597 | 38% helix, 19% strand | P29496 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 604 | 33% helix, 12% strand | P53091 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 663 | 29% helix, 14% strand | P38132 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · 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 | 863 | 0.88 | 0.91 | 134 | ATP |
| 2 | 776 | 0.88 | 0.91 | 117 | empty |
| 3 | 745 | 0.88 | 0.91 | 104 | empty |
| 4 | 1170 | 0.87 | 0.88 | 112 | empty |
| 5 | 974 | 0.87 | 0.88 | 101 | ATP |
Interfaces
35 interfaces between chains.
- 3–5 · 3825 Ų buried · 40 hydrogen bonds · protein-protein
- 4–6 · 3810 Ų buried · 39 hydrogen bonds · protein-protein
- 2–6 · 3666 Ų buried · 33 hydrogen bonds · protein-protein
- 4–7 · 3406 Ų buried · 35 hydrogen bonds · protein-protein
- 2–5 · 3249 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5U8S · Structure of eukaryotic CMG helicase at a replication fork · the same entry in another collection · chain 7 against 7, 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 Q12488
- Every structure of UniProt P40359
- Every structure of UniProt Q12146
- Every structure of UniProt Q03406
- Every structure of UniProt Q08032
- 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
- Elsewhere: RCSB PDB 5U8S · PDBe 5U8S · UniProt Q12488 · UniProt P40359 · UniProt Q12146 · UniProt Q03406 · UniProt Q08032 · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.