MolNFT v1 · #126211 · protein
Crystal structure of darpin-darpin rigid fusion, variant DD_232_11_D12 in complex JNK1A1 and JIP1 peptide
5LW1: “Crystal structure of darpin-darpin rigid fusion, variant DD_232_11_D12 in complex JNK1A1 and JIP1 peptide”. X-ray diffraction, 3 ligands (ADN, IVA, SO4), 15 pockets (best druggability 0.88). MolNFT v1 #126211 on GenesisL1: 3D…
- PDB
- 5LW1
- Type
- protein
- Length
- 2,045 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DD_232_11_D12; Mitogen-activated protein kinase 8; C-jun-amino-terminal…
- EC
- 2.7.11.24
- UniProt
- P45983, Q9UQF2
- Ligands
- ADN, IVA, SO4
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DD_232_11_D12 | protein | 320 | 54% helix, 0% strand | — |
| B, E, H | Mitogen-activated protein kinase 8 (EC 2.7.11.24) | protein | 355 | 38% helix, 17% strand | P45983 |
| C, F | C-jun-amino-terminal kinase-interacting protein 1 | protein | 9 | 0% helix, 0% strand | Q9UQF2 |
| D | DD_232_11_D12 | protein | 313 | 55% helix, 0% strand | — |
| G | DD_232_11_D12 | protein | 314 | 56% helix, 0% strand | — |
| I | C-jun-amino-terminal kinase-interacting protein 1 | protein | 10 | 0% helix, 0% strand | Q9UQF2 |
| L | Pepstatin | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADN · Adenosine · ligand · 3 copies · chains B, E, H
- IVA · Isovaleric acid · ligand · chains H, L
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, D, E, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.88 | 0.89 | 132 | ADN, SO4 |
| 2 | 758 | 0.86 | 0.89 | 90 | ADN, SO4 |
| 3 | 643 | 0.86 | 0.90 | 74 | ADN, SO4 |
| 4 | 687 | 0.84 | 0.88 | 108 | SO4 |
| 5 | 312 | 0.75 | 0.87 | 57 | empty |
Interfaces
19 interfaces between chains.
- E–G · 1540 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 1422 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1342 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 993 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 922 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (nonstandard, covalent ligand).
Compared structures
- 5LW1 · Crystal structure of DARPin-DARPin rigid fusion, variant DD_232_11_D12 in complex JNK1a1… · the same entry in another collection · chain L against L, TM-score 1.00
- P45983 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase 8 (P45983) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q9UQF2 · AlphaFold monomer V2.0 prediction for C-jun-amino-terminal kinase- interacting protein 1… · a predicted model of the same protein · chain C against A, TM-score 0.44
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 P45983
- Every structure of UniProt Q9UQF2
- Elsewhere: RCSB PDB 5LW1 · PDBe 5LW1 · UniProt P45983 · UniProt Q9UQF2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.