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High resolution crystal structure structure of HYHEL10 Fab complexed to hen egg lysozyme
Analyse High resolution crystal structure structure of HYHEL10 Fab complexed to hen egg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D9A
- Type
- protein
- Length
- 552 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C; Light chain of HYHEL10 antibody fragment (Fab); Heavy chain of HYHEL10…
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 11% strand | P00698 |
| L | Light chain of HYHEL10 antibody fragment (Fab) | protein | 213 | 7% helix, 51% strand | — |
| H | Heavy chain of HYHEL10 antibody fragment (Fab) | protein | 210 | 10% helix, 52% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.65 | 0.86 | 35 | empty |
| 2 | 425 | 0.56 | 0.74 | 45 | empty |
| 3 | 97 | 0.37 | 0.75 | 19 | empty |
| 4 | 55 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1846 Ų buried · 15 hydrogen bonds · protein-protein
- C–H · 577 Ų buried · 16 hydrogen bonds · protein-protein
- C–L · 420 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3D9A · High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme · 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 P00698
- Elsewhere: RCSB PDB 3D9A · PDBe 3D9A · UniProt P00698
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