Research workbench
Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex with mtx polyglutamate
Analyse Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L8W
- Type
- protein
- Length
- 1,722 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyl hydrolase
- EC
- 3.4.19.9
- UniProt
- Q6NY42
- Ligands
- DGL, MTX
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, I, B, E, G, K | Gamma-glutamyl hydrolase (EC 3.4.19.9) | protein | 287 | 36% helix, 26% strand | Q6NY42 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 4 copies · chains I, G
- MTX · Methotrexate · ligand · 2 copies · chains I, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.74 | 0.98 | 24 | empty |
| 2 | 68 | 0.74 | 0.98 | 19 | empty |
| 3 | 68 | 0.73 | 0.97 | 21 | empty |
| 4 | 251 | 0.64 | 0.82 | 35 | empty |
| 5 | 259 | 0.47 | 0.73 | 43 | empty |
Interfaces
6 interfaces between chains.
- B–G · 1756 Ų buried · 14 hydrogen bonds · protein-protein
- I–E · 1741 Ų buried · 14 hydrogen bonds · protein-protein
- D–K · 1729 Ų buried · 15 hydrogen bonds · protein-protein
- D–B · 471 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 453 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4L8W · Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex with MTX… · the same entry in another collection · chain B against B, 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 Q6NY42
- Elsewhere: RCSB PDB 4L8W · PDBe 4L8W · UniProt Q6NY42
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