MolNFT v1 · #151690 · protein + DNA + RNA
S. cerevisiae cmg-pol epsilon-DNA
6HV9 · DNA replication licensing factor MCM3: “S. cerevisiae cmg-pol epsilon-DNA”. Electron microscopy, 2 ligands (AGS, ZN), 20 pockets (best druggability 0.88). MolNFT v1 #151690 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6HV9
- Type
- protein + DNA + RNA
- Length
- 6,089 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication licensing factor MCM3; DNA replication licensing factor MCM4…
- EC
- 3.6.4.12, 2.7.7.7
- UniProt
- P24279, P30665, P29496, P53091, P29469, P38132, Q12488, P40359, Q12146, Q03406, Q08032, P24482, P21951
- Ligands
- AGS, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 16 distinct chains · 38% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 558 | 35% helix, 16% strand | P24279 |
| 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 589 | 33% helix, 14% strand | P30665 |
| 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 628 | 39% helix, 14% strand | P29496 |
| 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 571 | 35% helix, 10% strand | P53091 |
| 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 549 | 38% helix, 14% strand | P29469 |
| 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 616 | 33% helix, 14% strand | P38132 |
| C | DNA replication complex gins protein PSF1 | protein | 194 | 58% helix, 4% strand | Q12488 |
| D | DNA replication complex gins protein PSF2 | protein | 181 | 48% helix, 7% strand | P40359 |
| E | DNA replication complex gins protein PSF3 | protein | 159 | 54% helix, 6% strand | Q12146 |
| F | DNA replication complex gins protein SLD5 | protein | 218 | 53% helix, 5% strand | Q03406 |
| G | Cell division control protein 45 | protein | 541 | 47% helix, 4% strand | Q08032 |
| X | DNA/RNA (5'-R(*GP*CP*AP*GP*CP*CP*AP*CP*GP*C)-D(P*T)- R(P*GP*GP*CP*CP*G)-D(P*TP*TP*TP*T)-R(P*A)-3') | rna | 21 | — | — |
| Y | DNA/RNA (5'-D(P*T)- R(P*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*GP*CP*G)-D(P*T)-R(P*GP*GP*C)- D(P*T)-R(P*GP*C)-3') | rna | 21 | — | — |
| J | DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3') | dna | 7 | — | — |
| B | DNA polymerase epsilon subunit B (EC 2.7.7.7) | protein | 465 | 30% helix, 19% strand | P24482 |
| A | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 771 | 32% helix, 6% strand | P21951 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains 5, 2, 3
- ZN · Zinc ion · metal · 2 copies · chains A
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 | 1050 | 0.88 | 0.89 | 133 | empty |
| 2 | 1021 | 0.87 | 0.89 | 127 | empty |
| 3 | 1008 | 0.85 | 0.86 | 103 | empty |
| 4 | 774 | 0.84 | 0.87 | 128 | empty |
| 5 | 423 | 0.84 | 0.92 | 64 | empty |
Interfaces
43 interfaces between chains.
- 4–6 · 3668 Ų buried · 28 hydrogen bonds · protein-protein
- 3–5 · 3579 Ų buried · 25 hydrogen bonds · protein-protein
- 3–7 · 3184 Ų buried · 24 hydrogen bonds · protein-protein
- 5–2 · 2741 Ų buried · 23 hydrogen bonds · protein-protein
- 4–7 · 2511 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 6HV9 · S. cerevisiae CMG-Pol epsilon-DNA · the same entry in another collection · chain G against G, 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 P24279
- Every structure of UniProt P30665
- Every structure of UniProt P29496
- Every structure of UniProt P53091
- Every structure of UniProt P29469
- 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
- Every structure of UniProt P24482
- Every structure of UniProt P21951
- Elsewhere: RCSB PDB 6HV9 · PDBe 6HV9 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P29469 · UniProt P38132 · UniProt Q12488 · UniProt P40359 · UniProt Q12146 · UniProt Q03406 · UniProt Q08032 · UniProt P24482 · UniProt P21951
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