MolNFT v1 · #179648 · protein + DNA
Structure of the saccharomyces cerevisiae replicative polymerase delta in complex with a PRIMER/TEMPLATE and the PCNA clamp
7KC0 · DNA (5'- D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP…: “Structure of the saccharomyces cerevisiae replicative polymerase delta in complex with a PRIMER/TEMPLATE and…”. Electron microscopy, 4 ligands (SF4, D3T, MG), 20…
- PDB
- 7KC0
- Type
- protein + DNA
- Length
- 2,380 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)- 3'); DNA…
- EC
- 2.7.7.7
- UniProt
- A0A6B7JGY6, A0A6A5Q0V0, A0A6A5PTG9, A0A6A5PT00
- Ligands
- SF4, D3T, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'- D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)- 3') | dna | 21 | — | — |
| T | DNA (25-mer) | dna | 25 | — | — |
| F | Proliferating cell nuclear antigen | protein | 254 | 16% helix, 44% strand | A0A6B7JGY6 |
| A | DNA polymerase (EC 2.7.7.7) | protein | 1004 | 38% helix, 18% strand | A0A6A5Q0V0 |
| B | POL31 isoform 1 | protein | 463 | 20% helix, 22% strand | A0A6A5PTG9 |
| C | POL32 isoform 1 | protein | 109 | 27% helix, 18% strand | A0A6A5PT00 |
| E | Proliferating cell nuclear antigen | protein | 253 | 19% helix, 42% strand | A0A6B7JGY6 |
| G | Proliferating cell nuclear antigen | protein | 251 | 17% helix, 40% strand | A0A6B7JGY6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A, B
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains P, T, A
- MG · Magnesium ion · metal · 2 copies · chains P, A
- 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.83 | 0.84 | 94 | empty |
| 2 | 836 | 0.81 | 0.84 | 91 | MG, D3T |
| 3 | 1067 | 0.80 | 0.82 | 96 | empty |
| 4 | 133 | 0.75 | 0.93 | 35 | empty |
| 5 | 253 | 0.75 | 0.89 | 39 | empty |
Interfaces
14 interfaces between chains.
- B–C · 2616 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2478 Ų buried · 21 hydrogen bonds · protein-protein
- F–A · 1560 Ų buried · 9 hydrogen bonds · protein-protein
- T–A · 1357 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 947 Ų buried · 72 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7KC0 · Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a… · the same entry in another collection · chain P against P, 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 A0A6B7JGY6
- Every structure of UniProt A0A6A5Q0V0
- Every structure of UniProt A0A6A5PTG9
- Every structure of UniProt A0A6A5PT00
- Elsewhere: RCSB PDB 7KC0 · PDBe 7KC0 · UniProt A0A6B7JGY6 · UniProt A0A6A5Q0V0 · UniProt A0A6A5PTG9 · UniProt A0A6A5PT00
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.