MolNFT v1 · #163416 · protein
Cryo-EM structure of CTF18-1-8 in complex with the catalytic domain of DNA polymerase epsilon (class 2)
6S2F · DNA polymerase epsilon catalytic subunit a: “Cryo-EM structure of CTF18-1-8 in complex with the catalytic domain of DNA polymerase epsilon (class 2)”. Electron microscopy, 1 ligand (SF4), 20 pockets (best druggability 0.83). MolNFT…
- PDB
- 6S2F
- Type
- protein
- Length
- 1,539 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon catalytic subunit a; Chromosome transmission fidelity protein 8…
- EC
- 2.7.7.7
- UniProt
- P21951, P38877, P49956, P25559
- Ligands
- SF4
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 1006 | 41% helix, 22% strand | P21951 |
| D | Chromosome transmission fidelity protein 8 | protein | 132 | 11% helix, 54% strand | P38877 |
| E | Chromosome transmission fidelity protein 18 | protein | 26 | 15% helix, 38% strand | P49956 |
| B | Sister chromatid cohesion protein DCC1 | protein | 375 | 35% helix, 22% strand | P25559 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.83 | 0.84 | 128 | empty |
| 2 | 480 | 0.73 | 0.82 | 73 | empty |
| 3 | 55 | 0.73 | 0.98 | 19 | empty |
| 4 | 64 | 0.71 | 0.96 | 20 | empty |
| 5 | 61 | 0.69 | 0.96 | 25 | empty |
Interfaces
6 interfaces between chains.
- D–B · 2812 Ų buried · 63 hydrogen bonds · protein-protein
- D–E · 1096 Ų buried · 21 hydrogen bonds · protein-protein
- E–B · 954 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 687 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 620 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6S2F · Cryo-EM structure of Ctf18-1-8 in complex with the catalytic domain of DNA polymerase… · the same entry in another collection · chain B against B, TM-score 1.00
- P21951 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon catalytic subunit a (P21951) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P25559 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein DCC1 (P25559) · a predicted model of the same protein · chain B against A, TM-score 0.91
- P38877 · AlphaFold monomer V2.0 prediction for chromosome transmission fidelity protein 8 (P38877) · a predicted model of the same protein · chain D against A, TM-score 0.81
- P49956 · AlphaFold monomer V2.0 prediction for chromosome transmission fidelity protein 18 (P49956) · a predicted model of the same protein · chain E against A, TM-score 0.22
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 P21951
- Every structure of UniProt P38877
- Every structure of UniProt P49956
- Every structure of UniProt P25559
- Elsewhere: RCSB PDB 6S2F · PDBe 6S2F · UniProt P21951 · UniProt P38877 · UniProt P49956 · UniProt P25559
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