Research workbench
Heterotrimeric PCNA sliding clamp
Analyse Heterotrimeric PCNA sliding clamp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HII
- Type
- protein
- Length
- 1,470 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PCNA1 (SSO0397); PCNA2 (SSO1047); PCNA3 (SSO0405)
- UniProt
- P57766, Q97Z84, P57765
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, X | PCNA1 (SSO0397) | protein | 249 | 18% helix, 44% strand | P57766 |
| B, Y | PCNA2 (SSO1047) | protein | 243 | 21% helix, 48% strand | Q97Z84 |
| C, Z | PCNA3 (SSO0405) | protein | 243 | 22% helix, 44% strand | P57765 |
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.62 | 0.78 | 38 | empty |
| 2 | 105 | 0.47 | 0.79 | 19 | empty |
| 3 | 160 | 0.46 | 0.76 | 25 | empty |
| 4 | 152 | 0.46 | 0.76 | 22 | empty |
| 5 | 109 | 0.44 | 0.78 | 19 | empty |
Interfaces
7 interfaces between chains.
- X–Z · 725 Ų buried · 10 hydrogen bonds · protein-protein
- X–Y · 716 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 704 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 678 Ų buried · 10 hydrogen bonds · protein-protein
- C–X · 615 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 2HII · heterotrimeric PCNA sliding clamp · the same entry in another collection · chain Z against Z, TM-score 1.00
- P57765 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 3 (P57765) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q97Z84 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 2 (Q97Z84) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P57766 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 1 (P57766) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P57766
- Every structure of UniProt Q97Z84
- Every structure of UniProt P57765
- Elsewhere: RCSB PDB 2HII · PDBe 2HII · UniProt P57766 · UniProt Q97Z84 · UniProt P57765
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