MolNFT v1 · #101612 · protein
Crystal structure of the anti-human ngf Fab APE1531
4NWT · APE1531 ab Fab light chain: “Crystal structure of the anti-human ngf Fab APE1531”. X-ray diffraction, 5 pockets (best druggability 0.50). MolNFT v1 #101612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4NWT
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APE1531 ab Fab light chain; APE1531 ab Fab heavy chain
- UniProt
- Q8TCD0, P01857
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | APE1531 ab Fab light chain | protein | 220 | 6% helix, 52% strand | Q8TCD0 |
| H | APE1531 ab Fab heavy chain | protein | 232 | 5% helix, 52% strand | P01857 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains L, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains L, H
- PGE · Triethylene glycol · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.50 | 0.74 | 34 | empty |
| 2 | 126 | 0.44 | 0.77 | 20 | empty |
| 3 | 111 | 0.36 | 0.74 | 18 | empty |
| 4 | 83 | 0.35 | 0.75 | 19 | empty |
| 5 | 64 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 2111 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4NWT · Crystal structure of the anti-human NGF Fab APE1531 · the same entry in another collection · chain L against L, 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 Q8TCD0
- Every structure of UniProt P01857
- Elsewhere: RCSB PDB 4NWT · PDBe 4NWT · UniProt Q8TCD0 · UniProt P01857
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