Research workbench
Human polymerase delta-FEN1-PCNA toolbelt
Analyse Human polymerase delta-FEN1-PCNA toolbelt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TNZ
- Type
- protein + DNA
- Length
- 2,755 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase delta catalytic subunit; DNA polymerase delta subunit 2; DNA polymerase…
- EC
- 2.7.7.7, 3.1.11.-, 3.1.-.-
- UniProt
- P28340, P49005, Q15054, Q9HCU8, P12004, P39748
- Ligands
- SF4, TTP, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase delta catalytic subunit (EC 2.7.7.7, 3.1.11.-) | protein | 1010 | 35% helix, 19% strand | P28340 |
| B | DNA polymerase delta subunit 2 | protein | 431 | 20% helix, 23% strand | P49005 |
| C | DNA polymerase delta subunit 3 | protein | 143 | 37% helix, 22% strand | Q15054 |
| D | DNA polymerase delta subunit 4 | protein | 66 | 29% helix, 0% strand | Q9HCU8 |
| E | Proliferating cell nuclear antigen | protein | 251 | 18% helix, 44% strand | P12004 |
| F | Proliferating cell nuclear antigen | protein | 249 | 16% helix, 45% strand | P12004 |
| G | Proliferating cell nuclear antigen | protein | 249 | 18% helix, 45% strand | P12004 |
| H | Flap endonuclease 1 (EC 3.1.-.-) | protein | 306 | 41% helix, 11% strand | P39748 |
| P | DNA primer | dna | 23 | — | — |
| T | DNA template | dna | 27 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- TTP · Thymidine-5'-triphosphate · ligand · chains A, P, T
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.85 | 0.87 | 91 | empty |
| 2 | 147 | 0.81 | 0.96 | 28 | empty |
| 3 | 547 | 0.80 | 0.86 | 80 | SF4 |
| 4 | 88 | 0.78 | 0.98 | 20 | empty |
| 5 | 344 | 0.78 | 0.89 | 36 | empty |
Interfaces
18 interfaces between chains.
- B–C · 2648 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2101 Ų buried · 15 hydrogen bonds · protein-protein
- A–T · 1392 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–H · 1070 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 1054 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6TNZ · Human polymerase delta-FEN1-PCNA toolbelt · the same entry in another collection · chain T against T, TM-score 1.00
- Q15054 · AlphaFold monomer V2.0 prediction for DNA polymerase delta subunit 3 (Q15054) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P49005 · AlphaFold monomer V2.0 prediction for DNA polymerase delta subunit 2 (P49005) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P28340
- Every structure of UniProt P49005
- Every structure of UniProt Q15054
- Every structure of UniProt Q9HCU8
- Every structure of UniProt P12004
- Every structure of UniProt P39748
- Elsewhere: RCSB PDB 6TNZ · PDBe 6TNZ · UniProt P28340 · UniProt P49005 · UniProt Q15054 · UniProt Q9HCU8 · UniProt P12004 · UniProt P39748
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