Research workbench
PCNA from chaetomium thermophilum in complex with POLD4 pip peptide
Analyse PCNA from chaetomium thermophilum in complex with POLD4 pip peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O1F
- Type
- protein
- Length
- 1,525 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; Peptide fragment from POLD4
- UniProt
- G0SF70, G0RZ52
- Ligands
- NA
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 8 distinct chains · 19% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 253 | 19% helix, 45% strand | G0SF70 |
| B | Proliferating cell nuclear antigen | protein | 250 | 20% helix, 46% strand | G0SF70 |
| C | Proliferating cell nuclear antigen | protein | 238 | 21% helix, 45% strand | G0SF70 |
| D | Proliferating cell nuclear antigen | protein | 254 | 19% helix, 45% strand | G0SF70 |
| E | Proliferating cell nuclear antigen | protein | 246 | 20% helix, 47% strand | G0SF70 |
| F | Proliferating cell nuclear antigen | protein | 253 | 19% helix, 45% strand | G0SF70 |
| J, K, M | Peptide fragment from POLD4 | protein | 8 | 0% helix, 13% strand | G0RZ52 |
| O | Peptide fragment from POLD4 | protein | 7 | 0% helix, 14% strand | G0RZ52 |
Ligands and binding sites
- NA · Sodium ion · metal · 18 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.63 | 0.78 | 48 | empty |
| 2 | 190 | 0.61 | 0.82 | 31 | empty |
| 3 | 211 | 0.60 | 0.81 | 39 | empty |
| 4 | 200 | 0.59 | 0.81 | 35 | empty |
| 5 | 341 | 0.57 | 0.76 | 45 | empty |
Interfaces
16 interfaces between chains.
- B–D · 779 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 732 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 713 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 708 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 702 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7O1F · PCNA from Chaetomium thermophilum in complex with PolD4 PIP peptide · the same entry in another collection · chain A against A, 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 G0SF70
- Every structure of UniProt G0RZ52
- Elsewhere: RCSB PDB 7O1F · PDBe 7O1F · UniProt G0SF70 · UniProt G0RZ52
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