Research workbench
RFC:PCNA bound to dsdna with a ssdna gap of six nucleotides
Analyse RFC:PCNA bound to dsdna with a ssdna gap of six nucleotides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U1A
- Type
- protein + DNA
- Length
- 2,759 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 0.87
Structure
electron microscopy · 11 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor C subunit 1 | protein | 617 | 54% helix, 9% strand | P38630 |
| B | Replication factor C subunit 4 | protein | 319 | 61% helix, 10% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 327 | 57% helix, 8% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 340 | 60% helix, 8% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 337 | 55% helix, 13% strand | P38251 |
| F | Proliferating cell nuclear antigen | protein | 255 | 16% helix, 45% strand | P15873 |
| G | Proliferating cell nuclear antigen | protein | 257 | 17% helix, 44% strand | P15873 |
| H | Proliferating cell nuclear antigen | protein | 253 | 16% helix, 45% strand | P15873 |
| I | DNA - primer | dna | 15 | — | — |
| J | DNA - template | dna | 30 | — | — |
| K | DNA - non primer | dna | 9 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, C, 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 | 893 | 0.87 | 0.89 | 105 | empty |
| 2 | 751 | 0.84 | 0.87 | 98 | empty |
| 3 | 250 | 0.83 | 0.95 | 49 | ADP, MG |
| 4 | 446 | 0.82 | 0.90 | 59 | empty |
| 5 | 174 | 0.81 | 0.97 | 34 | AGS, MG |
Interfaces
30 interfaces between chains.
- A–E · 2966 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2895 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 2734 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2552 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2543 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7U1A · RFC:PCNA bound to dsDNA with a ssDNA gap of six nucleotides · the same entry in another collection · chain K against K, TM-score 1.00
- P38251 · AlphaFold monomer V2.0 prediction for replication factor C subunit 5 (P38251) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 7U1A · PDBe 7U1A · UniProt P38630 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P15873
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