MolNFT v1 · #147587 · protein + DNA
Modulation of PCNA sliding surface by P15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme
6EHT · Proliferating cell nuclear antigen: “Modulation of PCNA sliding surface by P15PAF suggests a suppressive mechanism for cisplatin-induced DNA…”. X-ray diffraction, 13 pockets (best druggability 0.82). MolNFT v1 #147587 on GenesisL1…
- PDB
- 6EHT
- Type
- protein + DNA
- Length
- 822 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; PCNA-associated factor; DNA…
- UniProt
- P12004, Q15004
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 254 | 19% helix, 46% strand | P12004 |
| B | Proliferating cell nuclear antigen | protein | 253 | 19% helix, 45% strand | P12004 |
| C | Proliferating cell nuclear antigen | protein | 256 | 19% helix, 46% strand | P12004 |
| D | PCNA-associated factor | protein | 20 | 15% helix, 5% strand | Q15004 |
| E | PCNA-associated factor | protein | 19 | 16% helix, 5% strand | Q15004 |
| F | DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3') | dna | 10 | — | — |
| G | DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3') | dna | 10 | — | — |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.82 | 0.98 | 31 | empty |
| 2 | 94 | 0.80 | 0.99 | 22 | empty |
| 3 | 51 | 0.71 | 0.98 | 21 | empty |
| 4 | 550 | 0.63 | 0.75 | 61 | empty |
| 5 | 248 | 0.60 | 0.80 | 33 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1009 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 887 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 637 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 504 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 463 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6EHT · Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for… · the same entry in another collection · chain G against G, TM-score 1.00
- Q15004 · AlphaFold monomer V2.0 prediction for PCNA-associated factor (Q15004) · a predicted model of the same protein · chain E against A, TM-score 0.32
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 P12004
- Every structure of UniProt Q15004
- Elsewhere: RCSB PDB 6EHT · PDBe 6EHT · UniProt P12004 · UniProt Q15004
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