MolNFT v1 · #188627 · protein + DNA
RFC:PCNA bound to nicked DNA
7U19 · Replication factor C subunit 1: “RFC:PCNA bound to nicked DNA”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #188627 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7U19
- Type
- protein + DNA
- Length
- 2,770 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, P15873
- Ligands
- AGS, ADP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor C subunit 1 | protein | 617 | 54% helix, 8% strand | P38630 |
| B | Replication factor C subunit 4 | protein | 319 | 60% helix, 9% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 328 | 57% helix, 9% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 338 | 60% helix, 9% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 338 | 54% helix, 13% strand | P38251 |
| F, G | Proliferating cell nuclear antigen | protein | 255 | 20% helix, 44% strand | P15873 |
| H | Proliferating cell nuclear antigen | protein | 253 | 18% helix, 41% strand | P15873 |
| I | Primer DNA | dna | 20 | — | — |
| J | Template DNA | dna | 34 | — | — |
| K | DNA | dna | 13 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D, E
- ADP · Adenosine-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 | 192 | 0.82 | 0.96 | 35 | AGS, MG |
| 2 | 188 | 0.81 | 0.96 | 35 | AGS, MG |
| 3 | 388 | 0.80 | 0.89 | 42 | empty |
| 4 | 469 | 0.79 | 0.87 | 47 | empty |
| 5 | 148 | 0.78 | 0.96 | 29 | AGS, MG |
Interfaces
33 interfaces between chains.
- A–E · 2935 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2790 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 2772 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2538 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2439 Ų buried · 27 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 P15873
- Elsewhere: RCSB PDB 7U19 · PDBe 7U19 · UniProt P38630 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P15873
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