MolNFT v1 · #140518 · protein
Crystal structure of human PCNA in complex with apim of human ZRANB3
5YD8 · Proliferating cell nuclear antigen: “Crystal structure of human PCNA in complex with apim of human ZRANB3”. X-ray diffraction, 3 pockets (best druggability 0.40). MolNFT v1 #140518 on GenesisL1: 3D structure, binding sites and…
- 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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