Research workbench
Crystal structure of gamma-glutamylcysteine synthetase complexed with aluminum fluoride
Analyse Crystal structure of gamma-glutamylcysteine synthetase complexed with aluminum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D33
- Type
- protein
- Length
- 2,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate--cysteine ligase
- EC
- 6.3.2.2
- UniProt
- P0A6W9
- Ligands
- GLU, CYS, ADP, AF3, MG
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate--cysteine ligase (EC 6.3.2.2) | protein | 510 | 52% helix, 13% strand | P0A6W9 |
| B | Glutamate--cysteine ligase (EC 6.3.2.2) | protein | 503 | 49% helix, 13% strand | P0A6W9 |
| C | Glutamate--cysteine ligase (EC 6.3.2.2) | protein | 504 | 50% helix, 13% strand | P0A6W9 |
| D | Glutamate--cysteine ligase (EC 6.3.2.2) | protein | 499 | 48% helix, 13% strand | P0A6W9 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- CYS · Cysteine · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- AF3 · Aluminum fluoride · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.85 | 0.86 | 127 | MG, GLU, CYS, ADP, AF3 |
| 2 | 1089 | 0.82 | 0.83 | 98 | MG, GLU, CYS, ADP, AF3 |
| 3 | 1127 | 0.79 | 0.80 | 93 | MG, GLU, CYS, ADP, AF3 |
| 4 | 336 | 0.78 | 0.89 | 38 | MG, GLU, CYS, AF3 |
| 5 | 674 | 0.75 | 0.81 | 59 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1011 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 964 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 553 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 531 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 361 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2D33 · Crystal Structure of gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride · the same entry in another collection · chain B against B, TM-score 1.00
- P0A6W9 · AlphaFold monomer V2.0 prediction for glutamate--cysteine ligase (P0A6W9) · a predicted model of the same protein · chain C 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 P0A6W9
- Elsewhere: RCSB PDB 2D33 · PDBe 2D33 · UniProt P0A6W9
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