MolNFT v1 · #127954 · protein
Crystal structure of the Fab fragment 22F12 in complex with 3- HYDROXYBENZO[A]PYRENE
5NBW · Fab 22F12 (L,H): “Crystal structure of the Fab fragment 22F12 in complex with 3- HYDROXYBENZO[A]PYRENE”. X-ray diffraction, 1 ligand (8SK), 8 pockets (best druggability 0.74). MolNFT v1 #127954 on GenesisL1: 3D structure, binding…
- PDB
- 5NBW
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 22F12 (L,H); Fab 22F12 (A,B)
- Ligands
- 8SK
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Fab 22F12 (L,H) | protein | 214 | 7% helix, 52% strand | — |
| H, B | Fab 22F12 (A,B) | protein | 216 | 8% helix, 49% strand | — |
Ligands and binding sites
- 8SK · benzo[a]pyren-3-ol · ligand · 2 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.74 | 0.78 | 78 | 8SK |
| 2 | 175 | 0.66 | 0.86 | 26 | empty |
| 3 | 114 | 0.65 | 0.88 | 19 | 8SK |
| 4 | 561 | 0.61 | 0.74 | 62 | empty |
| 5 | 393 | 0.57 | 0.75 | 50 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1890 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1787 Ų buried · 19 hydrogen bonds · protein-protein
- L–B · 320 Ų buried · 3 hydrogen bonds · protein-protein
- H–B · 198 Ų buried · 0 hydrogen bonds · protein-protein
- L–A · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5NBW · Crystal structure of the Fab fragment 22F12 in complex with 3-hydroxybenzo[a]pyrene · 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
- Elsewhere: RCSB PDB 5NBW · PDBe 5NBW
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