Research workbench
Trk-a in complex with ligand
Analyse Trk-a in complex with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PME
- Type
- protein
- Length
- 813 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity nerve growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P04629
- Ligands
- OOY, SRT, ZN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 268 | 42% helix, 18% strand | P04629 |
| B | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 271 | 43% helix, 18% strand | P04629 |
| C | High affinity nerve growth factor receptor (EC 2.7.10.1) | protein | 274 | 43% helix, 18% strand | P04629 |
Ligands and binding sites
- OOY · N-[2,4-bis(morpholin-4-yl)phenyl]-3-phenoxybenzamide · ligand · 3 copies · chains A, B, C
- SRT · S,R meso-tartaric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.77 | 0.80 | 93 | OOY |
| 2 | 629 | 0.75 | 0.81 | 59 | OOY |
| 3 | 329 | 0.73 | 0.85 | 32 | OOY |
| 4 | 453 | 0.63 | 0.76 | 45 | empty |
| 5 | 118 | 0.44 | 0.77 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 785 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 766 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6PME · Trk-a in complex with ligand · the same entry in another collection · chain A against A, TM-score 1.00
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 P04629
- Elsewhere: RCSB PDB 6PME · PDBe 6PME · UniProt P04629
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