Research workbench
Crystal structure of phage library-derived single-chain fv fragment 1F9 in complex with turkey egg-white lysozyme
Analyse Crystal structure of phage library-derived single-chain fv fragment 1F9 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DZB
- Type
- protein
- Length
- 702 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv fragment 1F9; Turkey egg-white lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00703
- Pockets
- 12 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Scfv fragment 1F9 | protein | 222 | 5% helix, 50% strand | — |
| X, Y | Turkey egg-white lysozyme C (EC 3.2.1.17) | protein | 129 | 37% helix, 11% strand | P00703 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.56 | 0.79 | 32 | empty |
| 2 | 78 | 0.56 | 0.87 | 19 | empty |
| 3 | 232 | 0.55 | 0.77 | 33 | empty |
| 4 | 137 | 0.40 | 0.74 | 24 | empty |
| 5 | 117 | 0.37 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–X · 901 Ų buried · 17 hydrogen bonds · protein-protein
- B–Y · 878 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1DZB · Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with… · the same entry in another collection · chain X against X, TM-score 1.00
- P00703 · AlphaFold monomer V2.0 prediction for lysozyme C (P00703) · a predicted model of the same protein · chain X against A, TM-score 0.98
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 P00703
- Elsewhere: RCSB PDB 1DZB · PDBe 1DZB · UniProt P00703
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