MolNFT v1 · #98416 · protein
Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex with mtx polyglutamate
4L8W · Gamma-glutamyl hydrolase: “Crystal structure of gamma glutamyl hydrolase (H218N) from zebrafish complex with mtx polyglutamate”. X-ray diffraction, 2 ligands (DGL, MTX), 17 pockets (best druggability 0.74). MolNFT v1 #98416 on…
- 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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