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2.4 ångström resolution crystal structure of shikimate 5-dehydrogenase (aroe) from vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH
Analyse 2.4 ångström resolution crystal structure of shikimate 5-dehydrogenase (aroe)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SEF
- Type
- protein
- Length
- 1,053 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate 5-dehydrogenase
- EC
- 1.1.1.25
- UniProt
- Q9KVT3
- Ligands
- NDP, SKM
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 268 | 43% helix, 20% strand | Q9KVT3 |
| B | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 269 | 44% helix, 19% strand | Q9KVT3 |
| C | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 244 | 40% helix, 19% strand | Q9KVT3 |
| D | Shikimate 5-dehydrogenase (EC 1.1.1.25) | protein | 272 | 40% helix, 21% strand | Q9KVT3 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SKM · (3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.72 | 0.79 | 69 | empty |
| 2 | 527 | 0.69 | 0.79 | 50 | SKM |
| 3 | 441 | 0.67 | 0.79 | 51 | SKM |
| 4 | 386 | 0.67 | 0.80 | 51 | empty |
| 5 | 247 | 0.62 | 0.81 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 949 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 806 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 486 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3SEF · 2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9KVT3 · AlphaFold monomer V2.0 prediction for shikimate dehydrogenase (NADP(+)) (Q9KVT3) · a predicted model of the same protein · chain A 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 Q9KVT3
- Elsewhere: RCSB PDB 3SEF · PDBe 3SEF · UniProt Q9KVT3
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