Research workbench
Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment
Analyse Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IC7
- Type
- protein
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase 7; Dual specificity mitogen-activated protein kinase…
- EC
- 2.7.11.24, 2.7.12.2
- UniProt
- Q13164, Q13163
- Ligands
- ANP
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase 7 (EC 2.7.11.24) | protein | 355 | 37% helix, 13% strand | Q13164 |
| D | Mitogen-activated protein kinase 7 (EC 2.7.11.24) | protein | 353 | 37% helix, 12% strand | Q13164 |
| E | Dual specificity mitogen-activated protein kinase kinase 5 (EC 2.7.12.2) | protein | 111 | 26% helix, 24% strand | Q13163 |
| B | Dual specificity mitogen-activated protein kinase kinase 5 (EC 2.7.12.2) | protein | 123 | 24% helix, 20% strand | Q13163 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.77 | 0.79 | 105 | empty |
| 2 | 1177 | 0.74 | 0.77 | 114 | empty |
| 3 | 338 | 0.69 | 0.82 | 36 | ANP |
| 4 | 300 | 0.67 | 0.82 | 40 | ANP |
| 5 | 79 | 0.61 | 0.89 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1907 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1532 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 12 hydrogen bonds · protein-protein
- D–B · 105 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 69 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4IC7 · Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment · the same entry in another collection · chain E against E, TM-score 1.00
- Q13164 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 7 (Q13164) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q13163 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain E against A, TM-score 0.86
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 Q13164
- Every structure of UniProt Q13163
- Elsewhere: RCSB PDB 4IC7 · PDBe 4IC7 · UniProt Q13164 · UniProt Q13163
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