Research workbench
Obody AM3L09 bound to hen egg-white lysozyme
Analyse Obody AM3L09 bound to hen egg-white lysozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GLV
- Type
- protein
- Length
- 941 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C; Obody AM3L09
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- PO4, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Lysozyme C (EC 3.2.1.17) | protein | 129 | 39% helix, 11% strand | P00698 |
| B, D, F | Obody AM3L09 | protein | 106 | 11% helix, 47% strand | — |
| H | Obody AM3L09 | protein | 107 | 11% helix, 47% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, D, E, F, G, H, C
- SO4 · Sulfate ion · ion · chains E
- GOL · Glycerol · additive · 20 copies · chains A, B, G, C, D, F, E, H
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.73 | 0.77 | 102 | PO4 |
| 2 | 807 | 0.73 | 0.78 | 87 | GOL |
| 3 | 405 | 0.60 | 0.76 | 42 | GOL |
| 4 | 133 | 0.41 | 0.75 | 20 | GOL |
| 5 | 102 | 0.37 | 0.75 | 19 | GOL |
Interfaces
13 interfaces between chains.
- G–H · 977 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 959 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 958 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 950 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 371 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4GLV · OBody AM3L09 bound to hen egg-white 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 4GLV · PDBe 4GLV · UniProt P00698
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