Research workbench
Crystal structure of hyhel-10 fv mutant (Y33AY53A) complexed with hen egg lysozyme
Analyse Crystal structure of hyhel-10 fv mutant (Y33AY53A) complexed with hen egg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DQF
- Type
- protein
- Length
- 700 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme binding ig kappa chain V23-J2 region; Ig VH,ANTI-lysozyme; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lysozyme binding ig kappa chain V23-J2 region | protein | 107 | 3% helix, 50% strand | — |
| B, E | Ig VH,ANTI-lysozyme | protein | 114 | 5% helix, 50% strand | — |
| C, F | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.83 | 0.85 | 127 | empty |
| 2 | 588 | 0.70 | 0.78 | 44 | empty |
| 3 | 61 | 0.34 | 0.77 | 17 | empty |
| 4 | 71 | 0.33 | 0.75 | 15 | empty |
| 5 | 54 | 0.32 | 0.78 | 14 | empty |
Interfaces
12 interfaces between chains.
- A–B · 802 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 780 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 436 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 422 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2DQF · Crystal structure of hyhel-10 FV mutant (y33ay53a) complexed with 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 2DQF · PDBe 2DQF · UniProt P00698
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