MolNFT v1 · #114442 · protein
Varying binding modes of inhibitors and structural differences in the binding pockets of different gamma-glutamyltranspeptidases
5BPK · Gamma-glutamyltranspeptidase (ggt): “Varying binding modes of inhibitors and structural differences in the binding pockets of different…”. X-ray diffraction, 1 ligand (4UD), 9 pockets (best druggability 0.84). MolNFT v1 #114442 on…
- PDB
- 5BPK
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltranspeptidase (ggt)
- UniProt
- O25743
- Ligands
- 4UD
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gamma-glutamyltranspeptidase (ggt) | protein | 348 | 48% helix, 13% strand | O25743 |
| C, D | Gamma-glutamyltranspeptidase (ggt) | protein | 188 | 20% helix, 26% strand | O25743 |
Ligands and binding sites
- 4UD · (2S)-amino[(5S)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid · ligand · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 43 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.84 | 0.90 | 90 | EDO |
| 2 | 489 | 0.69 | 0.80 | 47 | EDO |
| 3 | 51 | 0.67 | 0.97 | 24 | 4UD, EDO |
| 4 | 476 | 0.67 | 0.79 | 42 | EDO |
| 5 | 206 | 0.45 | 0.74 | 42 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 5886 Ų buried · 113 hydrogen bonds · protein-protein
- B–D · 5842 Ų buried · 112 hydrogen bonds · protein-protein
- C–B · 456 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 451 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 438 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5BPK · Varying binding modes of inhibitors and structural differences in the binding pockets of… · 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 O25743
- Elsewhere: RCSB PDB 5BPK · PDBe 5BPK · UniProt O25743
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