Research workbench
The crystal structure of G-type lysozyme from atlantic cod (gadus morhua L.) in complex with nag oligomers sheds new light on substrate binding and the catalytic mechanism. structure with nag to 1.7
Analyse The crystal structure of G-type lysozyme from atlantic cod (gadus morhua L.) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GXR
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Goose-type lysozyme 1
- EC
- 3.2.1.17
- UniProt
- B9TU22
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Goose-type lysozyme 1 (EC 3.2.1.17) | protein | 185 | 56% helix, 4% strand | B9TU22 |
| B | Goose-type lysozyme 1 (EC 3.2.1.17) | protein | 183 | 57% helix, 4% strand | B9TU22 |
| C | Goose-type lysozyme 1 (EC 3.2.1.17) | protein | 174 | 63% helix, 3% strand | B9TU22 |
| D | Goose-type lysozyme 1 (EC 3.2.1.17) | protein | 186 | 56% helix, 4% strand | B9TU22 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.75 | 0.77 | 96 | NAG |
| 2 | 184 | 0.58 | 0.81 | 30 | empty |
| 3 | 206 | 0.50 | 0.76 | 38 | NAG |
| 4 | 181 | 0.49 | 0.77 | 29 | NAG |
| 5 | 122 | 0.48 | 0.79 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 485 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 440 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 272 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 231 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 211 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3GXR · The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex… · 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 B9TU22
- Elsewhere: RCSB PDB 3GXR · PDBe 3GXR · UniProt B9TU22
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