MolNFT v1 · #188236 · protein + DNA
Structure of the yeast clamp loader (replication factor C rfc) bound to the sliding clamp (proliferating cell nuclear antigen PCNA) and primer-template DNA
7TID · Replication factor C subunit 1: “Structure of the yeast clamp loader (replication factor C rfc) bound to the sliding clamp (proliferating cell…”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.88).…
- PDB
- 7TID
- Type
- protein + DNA
- Length
- 2,614 residues
- Chains
- 10
- 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 0.88
Structure
electron microscopy · 10 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replication factor C subunit 1 | protein | 486 | 52% helix, 7% strand | P38630 |
| B | Replication factor C subunit 4 | protein | 319 | 61% helix, 9% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 327 | 58% helix, 8% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 340 | 59% helix, 8% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 338 | 54% helix, 13% strand | P38251 |
| F | Proliferating cell nuclear antigen | protein | 255 | 18% helix, 46% strand | P15873 |
| G | Proliferating cell nuclear antigen | protein | 254 | 16% helix, 44% strand | P15873 |
| H | Proliferating cell nuclear antigen | protein | 253 | 18% helix, 44% strand | P15873 |
| I | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*AP*TP*GP*TP*AP*CP*TP*CP*GP*TP*AP*GP*TP*GP*TP *CP*T)-3') | dna | 24 | — | — |
| J | DNA (5'- D(*AP*GP*AP*CP*AP*CP*TP*AP*CP*GP*AP*GP*TP*AP*CP*AP*TP*A)-3') | dna | 18 | — | — |
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 | 1026 | 0.88 | 0.89 | 126 | empty |
| 2 | 1027 | 0.87 | 0.88 | 122 | ADP |
| 3 | 485 | 0.83 | 0.90 | 73 | empty |
| 4 | 213 | 0.82 | 0.96 | 42 | AGS |
| 5 | 175 | 0.81 | 0.96 | 35 | AGS, MG |
Interfaces
33 interfaces between chains.
- A–E · 2968 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2878 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2864 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2515 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2431 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7TID · Structure of the yeast clamp loader (Replication Factor C RFC) bound to the sliding clamp… · the same entry in another collection · chain J against J, 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
- P40348 · AlphaFold monomer V2.0 prediction for replication factor C subunit 2 (P40348) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 7TID · PDBe 7TID · UniProt P38630 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P15873
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