Research workbench
Crystal structure of human gac in complex with glutamate and bptes
Analyse Crystal structure of human gac in complex with glutamate and bptes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UO9
- Type
- protein
- Length
- 1,624 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaminase kidney isoform, mitochondrial
- EC
- 3.5.1.2
- UniProt
- O94925
- Ligands
- 04A
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 411 | 50% helix, 11% strand | O94925 |
| B | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 401 | 50% helix, 11% strand | O94925 |
| C | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 404 | 49% helix, 11% strand | O94925 |
| D | Glutaminase kidney isoform, mitochondrial (EC 3.5.1.2) | protein | 408 | 50% helix, 11% strand | O94925 |
Ligands and binding sites
- 04A · N,N'-[sulfanediylbis(ethane-2,1-diyl-1,3,4-thiadiazole-5,2-diyl)]bis(2-phenylacetamide) · ligand · 2 copies · chains A, B, D, C
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.79 | 0.83 | 111 | empty |
| 2 | 1047 | 0.79 | 0.81 | 109 | empty |
| 3 | 492 | 0.70 | 0.80 | 49 | empty |
| 4 | 402 | 0.70 | 0.82 | 49 | empty |
| 5 | 174 | 0.61 | 0.83 | 25 | 04A |
Interfaces
5 interfaces between chains.
- A–C · 1929 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1841 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 638 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 612 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 62 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3UO9 · Crystal Structure of Human GAC in Complex with Glutamate and BPTES · the same entry in another collection · chain D against D, TM-score 1.00
- O94925 · AlphaFold monomer V2.0 prediction for glutaminase kidney isoform, mitochondrial (O94925) · a predicted model of the same protein · chain B 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 O94925
- Elsewhere: RCSB PDB 3UO9 · PDBe 3UO9 · UniProt O94925
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