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RIP2 kinase catalytic domain complex with 5-amino-1-phenylpyrazole-4- carboxamide.
Analyse RIP2 kinase catalytic domain complex with 5-amino-1-phenylpyrazole-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SZE
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 2
- EC
- 2.7.11.1
- UniProt
- O43353
- Ligands
- M2B, CA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1) | protein | 274 | 38% helix, 17% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1) | protein | 276 | 39% helix, 17% strand | O43353 |
Ligands and binding sites
- M2B · 5-Amino-1-Phenylpyrazole-4-Carboxamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.81 | 0.82 | 83 | empty |
| 2 | 321 | 0.66 | 0.81 | 38 | M2B |
| 3 | 214 | 0.64 | 0.83 | 30 | M2B |
| 4 | 113 | 0.45 | 0.78 | 23 | empty |
| 5 | 128 | 0.45 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1894 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6SZE · RIP2 Kinase Catalytic Domain complex with 5-Amino-1-Phenylpyrazole-4-Carboxamide. · the same entry in another collection · chain A against A, TM-score 1.00
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 O43353
- Elsewhere: RCSB PDB 6SZE · PDBe 6SZE · UniProt O43353
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