Research workbench
X-ray crystal structure of NDR1 kinase domain
Analyse X-ray crystal structure of NDR1 kinase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BXI
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase 38
- EC
- 2.7.11.1
- UniProt
- Q15208
- Ligands
- ANP, MG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase 38 (EC 2.7.11.1) | protein | 333 | 41% helix, 14% strand | Q15208 |
| B | SERINE/THREONINE-protein kinase 38 (EC 2.7.11.1) | protein | 332 | 41% helix, 14% strand | Q15208 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.84 | 0.93 | 45 | ANP, MG |
| 2 | 328 | 0.84 | 0.94 | 45 | ANP, MG |
| 3 | 770 | 0.68 | 0.75 | 72 | empty |
| 4 | 141 | 0.50 | 0.79 | 24 | empty |
| 5 | 118 | 0.48 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 442 Ų buried · 5 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 Q15208
- Elsewhere: RCSB PDB 6BXI · PDBe 6BXI · UniProt Q15208
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