MolNFT v1 · #123908 · protein
Ngf in complex with MEDI578 scfv
5JZ7 · Beta-nerve growth factor: “Ngf in complex with MEDI578 scfv”. X-ray diffraction, 19 pockets (best druggability 0.78). MolNFT v1 #123908 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JZ7
- Type
- protein
- Length
- 1,392 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-nerve growth factor; MEDI578 scfv, heavy chain; MEDI578 scfv, light chain
- UniProt
- P01138
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Beta-nerve growth factor | protein | 110 | 0% helix, 65% strand | P01138 |
| C, G, H, J | MEDI578 scfv, heavy chain | protein | 128 | 5% helix, 51% strand | — |
| D, I, K, L | MEDI578 scfv, light chain | protein | 110 | 5% helix, 48% strand | — |
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.78 | 0.83 | 75 | empty |
| 2 | 653 | 0.78 | 0.84 | 73 | empty |
| 3 | 107 | 0.77 | 0.96 | 29 | empty |
| 4 | 105 | 0.76 | 0.96 | 30 | empty |
| 5 | 185 | 0.52 | 0.78 | 23 | empty |
Interfaces
29 interfaces between chains.
- A–B · 1876 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1868 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 857 Ų buried · 10 hydrogen bonds · protein-protein
- G–I · 857 Ų buried · 9 hydrogen bonds · protein-protein
- J–K · 855 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5JZ7 · NGF IN COMPLEX WITH MEDI578 scFv · the same entry in another collection · chain H against H, 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 P01138
- Elsewhere: RCSB PDB 5JZ7 · PDBe 5JZ7 · UniProt P01138
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