MolNFT v1 · #140096 · protein
Crystal structure of RAD53 1-466 in complex with AMP-pnp
5XZV · SERINE/THREONINE-protein kinase RAD53: “Crystal structure of RAD53 1-466 in complex with AMP-pnp”. X-ray diffraction, 1 ligand (ANP), 9 pockets (best druggability 0.76). MolNFT v1 #140096 on GenesisL1: 3D structure, binding sites…
- PDB
- 5XZV
- Type
- protein
- Length
- 746 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase RAD53
- EC
- 2.7.12.1
- UniProt
- P22216
- Ligands
- ANP
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 375 | 32% helix, 27% strand | P22216 |
| B | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 371 | 32% helix, 23% strand | P22216 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.76 | 0.78 | 87 | ANP |
| 2 | 928 | 0.74 | 0.78 | 72 | ANP |
| 3 | 501 | 0.66 | 0.77 | 57 | empty |
| 4 | 197 | 0.47 | 0.75 | 29 | empty |
| 5 | 102 | 0.43 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1004 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5XZV · Crystal structure of Rad53 1-466 in complex with AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
- P22216 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase RAD53 (P22216) · a predicted model of the same protein · chain B 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 P22216
- Elsewhere: RCSB PDB 5XZV · PDBe 5XZV · UniProt P22216
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