MolNFT v2 · #222135 · protein
Cryo-EM map of human clmap-clamp loader ATAD5-RFC-gapped PCNA complex in intermediate state 3
8UI7 · ATPase family AAA domain-containing protein 5: “Cryo-EM map of human clmap-clamp loader ATAD5-RFC-gapped PCNA complex in intermediate state 3”. Electron microscopy at 4.2, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability…
- PDB
- 8UI7
- Type
- protein
- Length
- 2,760 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- Homo sapiens
- Molecule
- ATPase family AAA domain-containing protein 5; Replication factor C subunit 2…
- UniProt
- Q96QE3, P35250, P40937, P35249, P40938, P12004
- Ligands
- AGS, ADP, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 4.2 · 6 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATPase family AAA domain-containing protein 5 | protein | 643 | 47% helix, 6% strand | Q96QE3 |
| B | Replication factor C subunit 2 | protein | 319 | 61% helix, 8% strand | P35250 |
| C | Replication factor C subunit 5 | protein | 339 | 58% helix, 8% strand | P40937 |
| D | Replication factor C subunit 4 | protein | 328 | 58% helix, 7% strand | P35249 |
| E | Replication factor C subunit 3 | protein | 348 | 58% helix, 11% strand | P40938 |
| F, G, H | Proliferating cell nuclear antigen | protein | 261 | 18% helix, 41% strand | P12004 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, B, C
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains D, E
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
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 | 1096 | 0.88 | 0.89 | 123 | MG, AGS |
| 2 | 1013 | 0.86 | 0.87 | 112 | empty |
| 3 | 1146 | 0.85 | 0.85 | 145 | MG, AGS |
| 4 | 641 | 0.84 | 0.88 | 78 | MG, AGS |
| 5 | 151 | 0.82 | 0.97 | 39 | empty |
Interfaces
16 interfaces between chains.
- A–B · 4347 Ų buried · 38 hydrogen bonds · protein-protein
- A–E · 3950 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 2132 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1868 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1679 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- P40938 · AlphaFold monomer V2.0 prediction for replication factor C subunit 3 (P40938) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P40937 · AlphaFold monomer V2.0 prediction for replication factor C subunit 5 (P40937) · a predicted model of the same protein · chain C against A, TM-score 0.88
- Q96QE3 · AlphaFold monomer V2.0 prediction for ATPase family aaa domain- containing protein 5… · a predicted model of the same protein · chain A against A, TM-score 0.72
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 Q96QE3
- Every structure of UniProt P35250
- Every structure of UniProt P40937
- Every structure of UniProt P35249
- Every structure of UniProt P40938
- Every structure of UniProt P12004
- Elsewhere: RCSB PDB 8UI7 · PDBe 8UI7 · UniProt Q96QE3 · UniProt P35250 · UniProt P40937 · UniProt P35249 · UniProt P40938 · UniProt P12004
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.