Research workbench
Crystal structure of PCNA in complex with DNA polymerase iota fragment
Analyse Crystal structure of PCNA in complex with DNA polymerase iota fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZVM
- Type
- protein
- Length
- 776 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proliferating cell nuclear antigen; DNA polymerase iota
- EC
- 2.7.7.7
- UniProt
- P12004
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proliferating cell nuclear antigen | protein | 248 | 17% helix, 48% strand | P12004 |
| U | DNA polymerase iota (EC 2.7.7.7) | protein | 13 | 23% helix, 8% strand | — |
| B | Proliferating cell nuclear antigen | protein | 247 | 19% helix, 47% strand | P12004 |
| V | DNA polymerase iota (EC 2.7.7.7) | protein | 10 | 40% helix, 0% strand | — |
| C | Proliferating cell nuclear antigen | protein | 249 | 18% helix, 47% strand | P12004 |
| W | DNA polymerase iota (EC 2.7.7.7) | protein | 9 | 44% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.49 | 0.78 | 22 | empty |
| 2 | 103 | 0.42 | 0.77 | 21 | empty |
| 3 | 133 | 0.40 | 0.74 | 25 | empty |
| 4 | 95 | 0.36 | 0.75 | 21 | empty |
| 5 | 60 | 0.32 | 0.77 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–C · 757 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 750 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 736 Ų buried · 15 hydrogen bonds · protein-protein
- C–W · 560 Ų buried · 4 hydrogen bonds · protein-protein
- B–V · 547 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2ZVM · Crystal structure of PCNA in complex with DNA polymerase iota fragment · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 2ZVM · PDBe 2ZVM · UniProt P12004
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.