Research workbench
Open state of RFC:PCNA bound to a 3' SS/DSDNA junction (DNA2) without ntd
Analyse Open state of RFC:PCNA bound to a 3' SS/DSDNA junction (DNA2) without ntd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DR4
- Type
- protein + DNA
- Length
- 2,662 residues
- Chains
- 12
- 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, GDP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 12 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor C subunit 1 | protein | 497 | 56% 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 | 60% helix, 9% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 332 | 60% helix, 9% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 352 | 55% helix, 13% strand | P38251 |
| F | Proliferating cell nuclear antigen | protein | 257 | 19% helix, 46% strand | P15873 |
| G | Proliferating cell nuclear antigen | protein | 256 | 19% helix, 45% strand | P15873 |
| H | Proliferating cell nuclear antigen | protein | 258 | 17% helix, 39% strand | P15873 |
| I | DNA (5'- D(P*TP*TP*TP*CP*GP*GP*GP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*GP*G)-3') | dna | 19 | — | — |
| J | DNA (5'- D(P*CP*CP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*CP*CP*CP*GP*GP*C)-3') | dna | 18 | — | — |
| K | DNA (5'-D(P*AP*AP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') | dna | 12 | — | — |
| L | DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*TP*TP*T)-3') | dna | 13 | — | — |
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 | 1117 | 0.84 | 0.85 | 122 | empty |
| 2 | 605 | 0.84 | 0.89 | 79 | empty |
| 3 | 207 | 0.81 | 0.95 | 41 | MG, AGS |
| 4 | 415 | 0.81 | 0.90 | 68 | empty |
| 5 | 173 | 0.81 | 0.96 | 34 | MG, AGS |
Interfaces
34 interfaces between chains.
- A–E · 2982 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2697 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2630 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2593 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2491 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 8DR4 · Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD · the same entry in another collection · chain L against L, 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 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 8DR4 · PDBe 8DR4 · UniProt P38630 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P15873
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