MolNFT v1 · #141180 · protein
Cryo-EM structure of human atr-atrip complex
5YZ0 · SERINE/THREONINE-protein kinase atr: “Cryo-EM structure of human atr-atrip complex”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #141180 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YZ0
- Type
- protein
- Length
- 5,404 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase atr; Atr-interacting protein
- EC
- 2.7.11.1
- UniProt
- Q13535, Q8WXE1
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 60% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE-protein kinase atr (EC 2.7.11.1) | protein | 2362 | 63% helix, 1% strand | Q13535 |
| C | Atr-interacting protein | protein | 362 | 57% helix, 0% strand | Q8WXE1 |
| D | Atr-interacting protein | protein | 318 | 42% helix, 1% strand | Q8WXE1 |
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 | 961 | 0.86 | 0.87 | 127 | empty |
| 2 | 1063 | 0.83 | 0.84 | 131 | empty |
| 3 | 1006 | 0.83 | 0.84 | 117 | empty |
| 4 | 930 | 0.83 | 0.84 | 123 | empty |
| 5 | 867 | 0.82 | 0.85 | 73 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3296 Ų buried · 51 hydrogen bonds · protein-protein
- B–D · 616 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 603 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 582 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YZ0 · Cryo-EM Structure of human ATR-ATRIP complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q13535 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase atr (Q13535) · a predicted model of the same protein · chain B against A, TM-score 0.81
- Q8WXE1 · AlphaFold monomer V2.0 prediction for atr-interacting protein (Q8WXE1) · a predicted model of the same protein · chain C 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 Q13535
- Every structure of UniProt Q8WXE1
- Elsewhere: RCSB PDB 5YZ0 · PDBe 5YZ0 · UniProt Q13535 · UniProt Q8WXE1
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