MolNFT v1 · #191438 · protein + DNA
Open state of RFC:PCNA bound to a 3' SS/DSDNA junction
8DQX · Replication factor C subunit 1: “Open state of RFC:PCNA bound to a 3' SS/DSDNA junction”. Electron microscopy, 3 ligands (AGS, GDP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #191438 on GenesisL1: 3D structure, binding…
- PDB
- 8DQX
- Type
- protein + DNA
- Length
- 2,624 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, GDP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 11 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor C subunit 1 | protein | 497 | 57% helix, 7% strand | P38630 |
| B | Replication factor C subunit 4 | protein | 315 | 63% helix, 9% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 330 | 62% helix, 8% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 332 | 61% helix, 9% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 353 | 56% helix, 13% strand | P38251 |
| F | Proliferating cell nuclear antigen | protein | 257 | 21% helix, 45% strand | P15873 |
| G | Proliferating cell nuclear antigen | protein | 256 | 21% helix, 46% strand | P15873 |
| H | Proliferating cell nuclear antigen | protein | 258 | 19% helix, 45% strand | P15873 |
| I | DNA (5'-D(*TP*TP*TP*TP*TP*T)-3') | dna | 6 | — | — |
| J | DNA (5'-D(P*TP*CP*CP*GP*AP*GP*CP*GP*AP*A)-3') | dna | 10 | — | — |
| K | DNA (5'-D(P*TP*TP*TP*GP*CP*CP*CP*GP*GP*A)-3') | dna | 10 | — | — |
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 | 764 | 0.85 | 0.88 | 96 | empty |
| 2 | 514 | 0.84 | 0.90 | 52 | empty |
| 3 | 493 | 0.82 | 0.89 | 71 | empty |
| 4 | 173 | 0.81 | 0.97 | 32 | MG, AGS |
| 5 | 175 | 0.80 | 0.96 | 32 | MG, AGS |
Interfaces
25 interfaces between chains.
- A–E · 3069 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 2710 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2606 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2567 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2434 Ų buried · 42 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 8DQX · PDBe 8DQX · UniProt P38630 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P15873
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