MolNFT v1 · #21621 · protein
Crystal structure of 7S ngf: a complex of nerve growth factor with four binding proteins (serine proteinases)
1SGF: “Crystal structure of 7S ngf: a complex of nerve growth factor with four binding proteins (serine proteinases)”. X-ray diffraction, 2 ligands (NAG, ZN), 16 pockets (best druggability 0.78). MolNFT v1 #21621 on GenesisL1: 3D…
- PDB
- 1SGF
- Type
- protein
- Length
- 1,089 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nerve growth factor
- EC
- 3.4.21.35
- UniProt
- P00757, P01139, P00756
- Ligands
- NAG, ZN
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nerve growth factor (EC 3.4.21.35) | protein | 203 | 11% helix, 34% strand | P00757 |
| B | Nerve growth factor (EC 3.4.21.35) | protein | 109 | 0% helix, 60% strand | P01139 |
| G, Z | Nerve growth factor (EC 3.4.21.35) | protein | 232 | 13% helix, 36% strand | P00756 |
| X | Nerve growth factor (EC 3.4.21.35) | protein | 202 | 11% helix, 35% strand | P00757 |
| Y | Nerve growth factor (EC 3.4.21.35) | protein | 111 | 0% helix, 60% strand | P01139 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains G, B, Z, Y, A, X
- ZN · Zinc ion · metal · 2 copies · chains A, G, X, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.78 | 0.96 | 34 | empty |
| 2 | 149 | 0.78 | 0.95 | 36 | empty |
| 3 | 1148 | 0.77 | 0.79 | 75 | empty |
| 4 | 93 | 0.76 | 0.97 | 30 | empty |
| 5 | 129 | 0.74 | 0.94 | 24 | empty |
Interfaces
12 interfaces between chains.
- B–Y · 1503 Ų buried · 11 hydrogen bonds · protein-protein
- G–Z · 1113 Ų buried · 16 hydrogen bonds · protein-protein
- Y–Z · 846 Ų buried · 19 hydrogen bonds · protein-protein
- B–G · 831 Ų buried · 20 hydrogen bonds · protein-protein
- A–Y · 631 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1SGF · Crystal structure of 7S ngf: a complex of nerve growth factor with four binding proteins… · the same entry in another collection · chain Z against Z, TM-score 1.00
- P00756 · AlphaFold monomer V2.0 prediction for kallikrein 1-related peptidase B3 (P00756) · a predicted model of the same protein · chain G against A, TM-score 0.98
- P01139 · AlphaFold monomer V2.0 prediction for beta-nerve growth factor (P01139) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P00757 · AlphaFold monomer V2.0 prediction for kallikrein 1-related peptidase- like B4 (P00757) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P00757
- Every structure of UniProt P01139
- Every structure of UniProt P00756
- Elsewhere: RCSB PDB 1SGF · PDBe 1SGF · UniProt P00757 · UniProt P01139 · UniProt P00756
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