MolNFT v1 · #94964 · protein
Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment
4IC7 · Mitogen-activated protein kinase 7: “Crystal structure of the ERK5 kinase domain in complex with an MKK5 binding fragment”. X-ray diffraction, 1 ligand (ANP), 15 pockets (best druggability 0.77). MolNFT v1 #94964 on GenesisL1: 3D…
- 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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