MolNFT v1 · #61020 · protein
High resolution crystal structure structure of HYHEL10 Fab complexed to hen egg lysozyme
3D9A · Lysozyme C: “High resolution crystal structure structure of HYHEL10 Fab complexed to hen egg lysozyme”. X-ray diffraction, 4 pockets (best druggability 0.65). MolNFT v1 #61020 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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