MolNFT v1 · #34300 · protein
Crystal structure of gamma-glutamyltranspeptidase from escherichia COLI
2DBU: “Crystal structure of gamma-glutamyltranspeptidase from escherichia COLI”. X-ray diffraction, 6 pockets (best druggability 0.82). MolNFT v1 #34300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DBU
- Type
- protein
- Length
- 1,097 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltranspeptidase
- EC
- 2.3.2.2
- UniProt
- P18956
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 359 | 48% helix, 13% strand | P18956 |
| B, D | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 190 | 21% helix, 27% strand | P18956 |
| C | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 358 | 49% helix, 13% strand | P18956 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.82 | 0.83 | 74 | empty |
| 2 | 575 | 0.76 | 0.83 | 54 | empty |
| 3 | 519 | 0.75 | 0.83 | 52 | empty |
| 4 | 105 | 0.39 | 0.76 | 25 | empty |
| 5 | 50 | 0.31 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 6616 Ų buried · 121 hydrogen bonds · protein-protein
- C–D · 6539 Ų buried · 118 hydrogen bonds · protein-protein
- B–C · 502 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 449 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2DBU · Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli · the same entry in another collection · chain D against D, TM-score 1.00
- P18956 · AlphaFold monomer V2.0 prediction for glutathione hydrolase proenzyme (P18956) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P18956
- Elsewhere: RCSB PDB 2DBU · PDBe 2DBU · UniProt P18956
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