Research workbench
Crystal structure of human PCNA in complex with apim of human ZRANB3
Analyse Crystal structure of human PCNA in complex with apim of human ZRANB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YD8
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; ZRANB3
- EC
- 3.6.4.-, 3.1.-.-
- UniProt
- P12004, Q5FWF4
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | Proliferating cell nuclear antigen | protein | 243 | 20% helix, 47% strand | P12004 |
| X | Proliferating cell nuclear antigen | protein | 248 | 18% helix, 48% strand | P12004 |
| Z | Proliferating cell nuclear antigen | protein | 247 | 19% helix, 48% strand | P12004 |
| W | ZRANB3 (EC 3.6.4.-, 3.1.-.-) | protein | 8 | 38% helix, 0% strand | Q5FWF4 |
| U | ZRANB3 (EC 3.6.4.-, 3.1.-.-) | protein | 11 | 27% helix, 27% strand | Q5FWF4 |
| V | ZRANB3 (EC 3.6.4.-, 3.1.-.-) | protein | 7 | 43% helix, 0% strand | Q5FWF4 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.40 | 0.76 | 23 | empty |
| 2 | 109 | 0.38 | 0.75 | 19 | empty |
| 3 | 69 | 0.33 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- X–Z · 713 Ų buried · 16 hydrogen bonds · protein-protein
- Y–X · 707 Ų buried · 11 hydrogen bonds · protein-protein
- Y–Z · 703 Ų buried · 13 hydrogen bonds · protein-protein
- X–U · 682 Ų buried · 9 hydrogen bonds · protein-protein
- Z–W · 553 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5YD8 · Crystal structure of human PCNA in complex with APIM of human ZRANB3 · the same entry in another collection · chain V against V, TM-score 1.00
- Q5FWF4 · AlphaFold monomer V2.0 prediction for DNA annealing helicase and endonuclease ZRANB3… · a predicted model of the same protein · chain V against A, TM-score 0.71
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 Q5FWF4
- Elsewhere: RCSB PDB 5YD8 · PDBe 5YD8 · UniProt P12004 · UniProt Q5FWF4
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