Research workbench
LTK:ALKAL1 complex stabilized by a nanobody
Analyse LTK:ALKAL1 complex stabilized by a nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NX0
- Type
- protein
- Length
- 899 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leukocyte tyrosine kinase receptor; NB3.16; ALK and ltk ligand 1
- EC
- 2.7.10.1
- UniProt
- P29376, Q6UXT8
- Ligands
- NA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Leukocyte tyrosine kinase receptor (EC 2.7.10.1) | protein | 297 | 11% helix, 24% strand | P29376 |
| D | NB3.16 | protein | 120 | 5% helix, 48% strand | — |
| B | Leukocyte tyrosine kinase receptor (EC 2.7.10.1) | protein | 301 | 10% helix, 25% strand | P29376 |
| E | NB3.16 | protein | 123 | 2% helix, 49% strand | — |
| A | ALK and ltk ligand 1 | protein | 58 | 76% helix, 0% strand | Q6UXT8 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.83 | 0.84 | 135 | NA |
| 2 | 51 | 0.40 | 0.82 | 19 | empty |
| 3 | 120 | 0.37 | 0.73 | 22 | empty |
| 4 | 113 | 0.36 | 0.73 | 19 | empty |
| 5 | 76 | 0.34 | 0.75 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–B · 895 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 795 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 725 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 717 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 565 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7NX0 · LTK:ALKAL1 complex stabilized by a Nanobody · the same entry in another collection · chain A against A, TM-score 1.00
- P29376 · AlphaFold monomer V2.0 prediction for leukocyte tyrosine kinase receptor (P29376) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q6UXT8 · AlphaFold monomer V2.0 prediction for ALK and ltk ligand 1 (Q6UXT8) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P29376
- Every structure of UniProt Q6UXT8
- Elsewhere: RCSB PDB 7NX0 · PDBe 7NX0 · UniProt P29376 · UniProt Q6UXT8
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