MolNFT v1 · #111735 · protein
Humanized ROCO4 bound to LRRK2-IN1
4YZM · Probable SERINE/THREONINE-protein kinase ROCO4: “Humanized ROCO4 bound to LRRK2-IN1”. X-ray diffraction, 2 ligands (4K4, MG), 3 pockets (best druggability 0.65). MolNFT v1 #111735 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YZM
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable SERINE/THREONINE-protein kinase ROCO4
- EC
- 2.7.11.1
- UniProt
- Q6XHB2
- Ligands
- 4K4, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable SERINE/THREONINE-protein kinase ROCO4 (EC 2.7.11.1) | protein | 260 | 38% helix, 17% strand | Q6XHB2 |
| B | Probable SERINE/THREONINE-protein kinase ROCO4 (EC 2.7.11.1) | protein | 262 | 38% helix, 14% strand | Q6XHB2 |
Ligands and binding sites
- 4K4 · 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.65 | 0.85 | 26 | 4K4 |
| 2 | 246 | 0.63 | 0.82 | 34 | 4K4 |
| 3 | 498 | 0.58 | 0.74 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 128 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q6XHB2
- Elsewhere: RCSB PDB 4YZM · PDBe 4YZM · UniProt Q6XHB2
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