MolNFT v1 · #187718 · protein + DNA
Open state of RAD24-RFC:9-1-1 bound to a 5' SS/DSDNA junction
7ST9 · Checkpoint protein RAD24: “Open state of RAD24-RFC:9-1-1 bound to a 5' SS/DSDNA junction”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #187718 on GenesisL1: 3D structure, binding…
- PDB
- 7ST9
- Type
- protein + DNA
- Length
- 2,837 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Checkpoint protein RAD24; Replication factor C subunit 4; Replication factor C subunit 3…
- UniProt
- P32641, P40339, P38629, P40348, P38251, P48581, Q08949, Q02574
- Ligands
- AGS, ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 10 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Checkpoint protein RAD24 | protein | 522 | 56% helix, 6% strand | P32641 |
| B | Replication factor C subunit 4 | protein | 315 | 62% helix, 9% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 327 | 61% helix, 9% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 335 | 59% helix, 9% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 354 | 56% helix, 14% strand | P38251 |
| F | DNA damage checkpoint control protein RAD17 | protein | 293 | 23% helix, 43% strand | P48581 |
| G | DNA damage checkpoint protein 1 | protein | 340 | 25% helix, 39% strand | Q08949 |
| H | DNA damage checkpoint control protein MEC3 | protein | 316 | 25% helix, 38% strand | Q02574 |
| J | DNA (50-mer) | dna | 25 | — | — |
| I | DNA (5'- D(P*CP*GP*CP*TP*CP*CP*TP*TP*CP*CP*TP*GP*AP*CP*TP*CP*GP*TP*CP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · chains 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 | 578 | 0.83 | 0.89 | 69 | ADP |
| 2 | 220 | 0.82 | 0.96 | 36 | MG, AGS |
| 3 | 198 | 0.82 | 0.96 | 43 | MG, AGS |
| 4 | 579 | 0.81 | 0.87 | 53 | empty |
| 5 | 769 | 0.81 | 0.85 | 79 | empty |
Interfaces
24 interfaces between chains.
- A–E · 3287 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 2829 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2673 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2472 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2415 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7ST9 · Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction · the same entry in another collection · chain I against I, TM-score 1.00
- Q08949 · AlphaFold monomer V2.0 prediction for DNA damage checkpoint protein 1 (Q08949) · a predicted model of the same protein · chain G 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 0.96
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 P32641
- Every structure of UniProt P40339
- Every structure of UniProt P38629
- Every structure of UniProt P40348
- Every structure of UniProt P38251
- Every structure of UniProt P48581
- Every structure of UniProt Q08949
- Every structure of UniProt Q02574
- Elsewhere: RCSB PDB 7ST9 · PDBe 7ST9 · UniProt P32641 · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt P48581 · UniProt Q08949 · UniProt Q02574
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