MolNFT v1 · #56702 · protein
5-fluorotryptophan incorporated SCFV10 complexed to hen egg lysozyme
2ZNX: “5-fluorotryptophan incorporated SCFV10 complexed to hen egg lysozyme”. X-ray diffraction, 1 ligand (1PG), 11 pockets (best druggability 0.75). MolNFT v1 #56702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZNX
- Type
- protein
- Length
- 700 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- 1PG
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Scfv | protein | 221 | 5% helix, 50% strand | — |
| Y, Z | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
Ligands and binding sites
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, Y, B, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.75 | 0.85 | 67 | empty |
| 2 | 168 | 0.66 | 0.86 | 28 | 1PG |
| 3 | 197 | 0.65 | 0.84 | 33 | 1PG |
| 4 | 96 | 0.38 | 0.75 | 19 | empty |
| 5 | 84 | 0.37 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–Z · 970 Ų buried · 24 hydrogen bonds · protein-protein
- A–Y · 949 Ų buried · 27 hydrogen bonds · protein-protein
- Y–B · 499 Ų buried · 7 hydrogen bonds · protein-protein
- A–Z · 496 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 modified (disulfide, nonstandard).
Compared structures
- 2ZNX · 5-Fluorotryptophan Incorporated ScFv10 Complexed to Hen Egg Lysozyme · the same entry in another collection · chain A against A, 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 P00698
- Elsewhere: RCSB PDB 2ZNX · PDBe 2ZNX · UniProt P00698
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