MolNFT v1 · #59323 · protein
Crystal structure of the neurotrophin-3 and P75NTR symmetrical complex
3BUK: “Crystal structure of the neurotrophin-3 and P75NTR symmetrical complex”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.81). MolNFT v1 #59323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BUK
- Type
- protein
- Length
- 540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurotrophin-3; Tumor necrosis factor receptor superfamily member 16
- UniProt
- P20783, P07174
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurotrophin-3 | protein | 111 | 0% helix, 58% strand | P20783 |
| C, D | Tumor necrosis factor receptor superfamily member 16 | protein | 159 | 0% helix, 31% strand | P07174 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.81 | 0.83 | 102 | empty |
| 2 | 97 | 0.77 | 0.97 | 30 | empty |
| 3 | 528 | 0.75 | 0.83 | 61 | empty |
| 4 | 168 | 0.60 | 0.83 | 32 | empty |
| 5 | 99 | 0.55 | 0.85 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1513 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 861 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 824 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 526 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3BUK · Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex · the same entry in another collection · chain C against C, TM-score 1.00
- P20783 · AlphaFold monomer V2.0 prediction for neurotrophin-3 (P20783) · a predicted model of the same protein · chain A against A, TM-score 0.87
- P07174 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain C 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 P20783
- Every structure of UniProt P07174
- Elsewhere: RCSB PDB 3BUK · PDBe 3BUK · UniProt P20783 · UniProt P07174
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