Research workbench
Complex between HYHEL10 Fab fragment heavy chain mutant I29F and pekin duck egg lysozyme isoform I (del-I)
Analyse Complex between HYHEL10 Fab fragment heavy chain mutant I29F and pekin duck egg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJO
- Type
- protein
- Length
- 1,092 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HYHEL10 heavy chain Fab fragment carrying I29F mutation.; HYHEL10 light chain Fab…
- EC
- 3.2.1.18
- UniProt
- U3J0P1
- Ligands
- NA, CL
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HYHEL10 heavy chain Fab fragment carrying I29F mutation. (EC 3.2.1.18) | protein | 206 | 6% helix, 52% strand | — |
| B, D | HYHEL10 light chain Fab fragment | protein | 211 | 6% helix, 55% strand | — |
| C | HYHEL10 heavy chain Fab fragment carrying I29F mutation. (EC 3.2.1.18) | protein | 208 | 6% helix, 51% strand | — |
| E | Lysozyme isoform I (del-I) | protein | 127 | 41% helix, 11% strand | U3J0P1 |
| F | Lysozyme isoform I (del-I) | protein | 129 | 40% helix, 11% strand | U3J0P1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.72 | 0.80 | 66 | empty |
| 2 | 855 | 0.71 | 0.77 | 70 | empty |
| 3 | 837 | 0.70 | 0.76 | 77 | empty |
| 4 | 114 | 0.51 | 0.81 | 23 | empty |
| 5 | 135 | 0.49 | 0.79 | 22 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1654 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1648 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 871 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 530 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 511 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5VJO · Complex between HyHEL10 Fab fragment heavy chain mutant I29F and Pekin duck 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 U3J0P1
- Elsewhere: RCSB PDB 5VJO · PDBe 5VJO · UniProt U3J0P1
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