Research workbench
Crystal structure of gamma-glutamyl hydrolase (C108A) complex with mtx
Analyse Crystal structure of gamma-glutamyl hydrolase (C108A) complex with mtx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L8F
- Type
- protein
- Length
- 1,148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyl hydrolase
- EC
- 3.4.19.9
- UniProt
- Q6NY42
- Ligands
- MTX
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, B, A | Gamma-glutamyl hydrolase (EC 3.4.19.9) | protein | 287 | 37% helix, 27% strand | Q6NY42 |
Ligands and binding sites
- MTX · Methotrexate · ligand · 2 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.76 | 0.98 | 23 | empty |
| 2 | 78 | 0.75 | 0.98 | 24 | empty |
| 3 | 767 | 0.73 | 0.78 | 73 | empty |
| 4 | 541 | 0.69 | 0.79 | 44 | empty |
| 5 | 208 | 0.49 | 0.75 | 36 | MTX |
Interfaces
4 interfaces between chains.
- C–D · 1715 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1711 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 641 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4L8F · Crystal structure of gamma-glutamyl hydrolase (C108A) complex with MTX · the same entry in another collection · chain D against D, 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 4L8F · PDBe 4L8F · UniProt Q6NY42
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