Research workbench
Crystal structure of aspartate semialdehyde dehydrogenase II complexed with asa from vibrio cholerae
Analyse Crystal structure of aspartate semialdehyde dehydrogenase II complexed with asa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R00
- Type
- protein
- Length
- 944 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate-semialdehyde dehydrogenase
- EC
- 1.2.1.11
- UniProt
- P23247
- Ligands
- OEG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 306 | 34% helix, 30% strand | P23247 |
| B | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 302 | 36% helix, 31% strand | P23247 |
| C | Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) | protein | 336 | 37% helix, 25% strand | P23247 |
Ligands and binding sites
- OEG · 2,2'-oxydiacetic acid · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.81 | 0.98 | 35 | empty |
| 2 | 763 | 0.80 | 0.84 | 83 | OEG |
| 3 | 286 | 0.72 | 0.86 | 51 | empty |
| 4 | 96 | 0.57 | 0.86 | 26 | empty |
| 5 | 111 | 0.56 | 0.84 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1927 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1112 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 140 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 2R00 · crystal structure of aspartate semialdehyde dehydrogenase II complexed with ASA from… · the same entry in another collection · chain A against A, TM-score 1.00
- P23247 · AlphaFold monomer V2.0 prediction for aspartate-semialdehyde dehydrogenase 2 (P23247) · 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 P23247
- Elsewhere: RCSB PDB 2R00 · PDBe 2R00 · UniProt P23247
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