Research workbench
RAD24-rfc ADP state
Analyse RAD24-rfc ADP state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7STE
- Type
- protein
- Length
- 1,774 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication factor C subunit 4; Replication factor C subunit 3; Replication factor C…
- UniProt
- P40339, P38629, P40348, P38251, P32641
- Ligands
- ADP, ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Replication factor C subunit 4 | protein | 315 | 57% helix, 8% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 324 | 61% helix, 9% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 327 | 60% helix, 8% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 340 | 56% helix, 13% strand | P38251 |
| A | Checkpoint protein RAD24 | protein | 468 | 57% helix, 5% strand | P32641 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains B, C, D, E
- ATP · Adenosine-5'-triphosphate · ligand · chains B, A
- MG · Magnesium ion · metal · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.86 | 0.87 | 107 | ADP |
| 2 | 1064 | 0.78 | 0.80 | 95 | ADP |
| 3 | 254 | 0.75 | 0.89 | 41 | ADP |
| 4 | 459 | 0.74 | 0.84 | 62 | ADP |
| 5 | 481 | 0.70 | 0.80 | 36 | empty |
Interfaces
6 interfaces between chains.
- E–A · 3197 Ų buried · 32 hydrogen bonds · protein-protein
- B–A · 2309 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1839 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1783 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1778 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 7STE · Rad24-RFC ADP state · the same entry in another collection · chain A against A, 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 0.99
- 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 0.90
- P40339 · AlphaFold monomer V2.0 prediction for replication factor C subunit 4 (P40339) · a predicted model of the same protein · chain B against A, TM-score 0.88
- P38629 · AlphaFold monomer V2.0 prediction for replication factor C subunit 3 (P38629) · a predicted model of the same protein · chain C against A, TM-score 0.86
- P32641 · AlphaFold monomer V2.0 prediction for checkpoint protein RAD24 (P32641) · a predicted model of the same protein · chain A against A, TM-score 0.54
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 P40339
- Every structure of UniProt P38629
- Every structure of UniProt P40348
- Every structure of UniProt P38251
- Every structure of UniProt P32641
- Elsewhere: RCSB PDB 7STE · PDBe 7STE · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P32641
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