Research workbench
Crystal structure of ERK2 in complex with an adenosine derivative
Analyse Crystal structure of ERK2 in complex with an adenosine derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FLV
- Type
- protein
- Length
- 345 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 1
- EC
- 2.7.11.24
- UniProt
- P63086
- Ligands
- DTW, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 1 (EC 2.7.11.24) | protein | 345 | 40% helix, 15% strand | P63086 |
Ligands and binding sites
- DTW · [(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-(4-diazanyl-4-oxidanylidene-butyl)sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino-azanylidene-azanium · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.66 | 0.78 | 37 | DTW |
| 2 | 75 | 0.54 | 0.86 | 17 | empty |
| 3 | 113 | 0.54 | 0.83 | 19 | empty |
| 4 | 53 | 0.32 | 0.77 | 15 | DMS |
| 5 | 50 | 0.29 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 6FLV · Crystal structure of ERK2 in complex with an adenosine derivative · the same entry in another collection · chain A against A, TM-score 1.00
- P63086 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 1 (P63086) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P63086
- Elsewhere: RCSB PDB 6FLV · PDBe 6FLV · UniProt P63086
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