MolNFT v1 · #160759 · protein
Structure of CTF4 trimer in complex with two cmg helicases
6PTN · DNA polymerase alpha-binding protein: “Structure of CTF4 trimer in complex with two cmg helicases”. Electron microscopy, 1 ligand (ATP), 20 pockets (best druggability 0.89). MolNFT v1 #160759 on GenesisL1: 3D structure, binding…
- PDB
- 6PTN
- Type
- protein
- Length
- 11,517 residues
- Chains
- 25
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase alpha-binding protein; DNA replication complex gins protein PSF1; DNA…
- EC
- 3.6.4.12
- UniProt
- Q01454, Q12488, P40359, Q12146, Q03406, Q08032, P29469, P24279, P30665, P29496, P53091, P38132
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 13 distinct chains · 32% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, G | DNA polymerase alpha-binding protein | protein | 424 | 25% helix, 30% strand | Q01454 |
| F | DNA polymerase alpha-binding protein | protein | 431 | 25% helix, 29% strand | Q01454 |
| a, A | DNA replication complex gins protein PSF1 | protein | 208 | 51% helix, 5% strand | Q12488 |
| b, B | DNA replication complex gins protein PSF2 | protein | 181 | 41% helix, 7% strand | P40359 |
| c, C | DNA replication complex gins protein PSF3 | protein | 159 | 47% helix, 6% strand | Q12146 |
| d, D | DNA replication complex gins protein SLD5 | protein | 234 | 51% helix, 5% strand | Q03406 |
| h, H | Cell division control protein 45 | protein | 553 | 42% helix, 8% strand | Q08032 |
| i, 2 | DNA replication licensing factor MCM2 (EC 3.6.4.12) | protein | 634 | 31% helix, 7% strand | P29469 |
| j, 3 | DNA replication licensing factor MCM3 (EC 3.6.4.12) | protein | 594 | 29% helix, 14% strand | P24279 |
| k, 4 | DNA replication licensing factor MCM4 (EC 3.6.4.12) | protein | 682 | 30% helix, 12% strand | P30665 |
| l, 5 | Minichromosome maintenance protein 5 (EC 3.6.4.12) | protein | 597 | 31% helix, 13% strand | P29496 |
| m, 6 | DNA replication licensing factor MCM6 (EC 3.6.4.12) | protein | 614 | 29% helix, 10% strand | P53091 |
| n, 7 | DNA replication licensing factor MCM7 (EC 3.6.4.12) | protein | 663 | 27% helix, 10% strand | P38132 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains i, m, j, l, 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 | 886 | 0.89 | 0.92 | 126 | empty |
| 2 | 1035 | 0.88 | 0.89 | 140 | empty |
| 3 | 779 | 0.87 | 0.90 | 91 | empty |
| 4 | 1003 | 0.87 | 0.89 | 115 | ATP |
| 5 | 1126 | 0.87 | 0.88 | 131 | empty |
Interfaces
57 interfaces between chains.
- k–m · 3851 Ų buried · 25 hydrogen bonds · protein-protein
- 4–6 · 3849 Ų buried · 25 hydrogen bonds · protein-protein
- j–l · 3691 Ų buried · 27 hydrogen bonds · protein-protein
- 3–5 · 3688 Ų buried · 27 hydrogen bonds · protein-protein
- i–m · 3536 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PTN · Structure of Ctf4 trimer in complex with two CMG helicases · the same entry in another collection · chain l against l, 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 Q01454
- 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 6PTN · PDBe 6PTN · UniProt Q01454 · UniProt Q12488 · UniProt P40359 · UniProt Q12146 · UniProt Q03406 · UniProt Q08032 · UniProt P29469 · UniProt P24279 · UniProt P30665 · UniProt P29496 · UniProt P53091 · UniProt P38132
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