MolNFT v1 · #191446 · protein + DNA
Open state of RFC:PCNA bound to a nicked dsdna
8DR7 · Replication factor C subunit 1: “Open state of RFC:PCNA bound to a nicked dsdna”. Electron microscopy, 3 ligands (AGS, GDP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #191446 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8DR7
- Type
- protein + DNA
- Length
- 2,649 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication factor C subunit 1; Replication factor C subunit 4; Replication factor C…
- UniProt
- P38630, P40339, P38629, P40348, P38251, A0A6B7JGY6
- Ligands
- AGS, GDP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor C subunit 1 | protein | 497 | 54% helix, 7% strand | P38630 |
| B | Replication factor C subunit 4 | protein | 318 | 60% helix, 9% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 330 | 61% helix, 9% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 332 | 59% helix, 9% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 352 | 55% helix, 14% strand | P38251 |
| F | Proliferating cell nuclear antigen | protein | 257 | 19% helix, 47% strand | A0A6B7JGY6 |
| G | Proliferating cell nuclear antigen | protein | 256 | 18% helix, 43% strand | A0A6B7JGY6 |
| H | Proliferating cell nuclear antigen | protein | 258 | 16% helix, 38% strand | A0A6B7JGY6 |
| I | DNA (26-mer) | dna | 26 | — | — |
| J | DNA (5'-D(P*GP*GP*CP*CP*CP*CP*CP*CP*CP*GP*GP*C)-3') | dna | 12 | — | — |
| K | DNA (5'-D(P*AP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D, E
- GDP · Guanosine-5'-diphosphate · ligand · chains A, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E
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 | 830 | 0.86 | 0.89 | 112 | empty |
| 2 | 1105 | 0.86 | 0.87 | 113 | GDP |
| 3 | 187 | 0.81 | 0.96 | 32 | MG, AGS |
| 4 | 199 | 0.81 | 0.95 | 31 | MG, AGS |
| 5 | 196 | 0.81 | 0.95 | 35 | MG, AGS |
Interfaces
30 interfaces between chains.
- A–E · 2970 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2720 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2688 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2547 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2492 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
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 P38630
- Every structure of UniProt P40339
- Every structure of UniProt P38629
- Every structure of UniProt P40348
- Every structure of UniProt P38251
- Every structure of UniProt A0A6B7JGY6
- Elsewhere: RCSB PDB 8DR7 · PDBe 8DR7 · UniProt P38630 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt A0A6B7JGY6
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