Research workbench
Obody AM3L15 bound to hen egg-white lysozyme
Analyse Obody AM3L15 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
- 4GN5
- Type
- protein
- Length
- 478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Obody AM3L15; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Obody AM3L15 | protein | 113 | 14% helix, 41% strand | — |
| B | Obody AM3L15 | protein | 107 | 15% helix, 43% strand | — |
| C, D | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains C, D
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.35 | 0.77 | 14 | empty |
| 2 | 95 | 0.33 | 0.73 | 20 | empty |
| 3 | 52 | 0.28 | 0.75 | 14 | empty |
| 4 | 52 | 0.26 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–C · 947 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 934 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 308 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 198 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4GN5 · OBody AM3L15 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 4GN5 · PDBe 4GN5 · UniProt P00698
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