Research workbench
Structure of human PCNA bound to RNASEH2B pip box peptide
Analyse Structure of human PCNA bound to RNASEH2B pip box peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P87
- Type
- protein
- Length
- 1,539 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; Ribonuclease H2 subunit B
- UniProt
- P12004, Q5TBB1
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Proliferating cell nuclear antigen | protein | 245 | 20% helix, 47% strand | P12004 |
| G, J, L | Ribonuclease H2 subunit B | protein | 11 | 27% helix, 18% strand | Q5TBB1 |
| H, I, K | Ribonuclease H2 subunit B | protein | 12 | 25% helix, 17% strand | Q5TBB1 |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.64 | 0.82 | 25 | empty |
| 2 | 255 | 0.63 | 0.82 | 26 | empty |
| 3 | 241 | 0.63 | 0.82 | 27 | empty |
| 4 | 273 | 0.60 | 0.79 | 30 | empty |
| 5 | 243 | 0.59 | 0.80 | 25 | empty |
Interfaces
27 interfaces between chains.
- E–K · 702 Ų buried · 7 hydrogen bonds · protein-protein
- C–I · 699 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 699 Ų buried · 7 hydrogen bonds · protein-protein
- F–L · 663 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 662 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3P87 · Structure of human PCNA bound to RNASEH2B PIP box peptide · 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 P12004
- Every structure of UniProt Q5TBB1
- Elsewhere: RCSB PDB 3P87 · PDBe 3P87 · UniProt P12004 · UniProt Q5TBB1
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