Research workbench
Crystal structure of lysy from thermus thermophilus complexed with NADP+ and lysw-gamma-aminoadipic semialdehyde
Analyse Crystal structure of lysy from thermus thermophilus complexed with NADP+ and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EIO
- Type
- protein
- Length
- 732 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-gamma-glutamyl-PHOSPHATE/N-acetyl-gamma- aminoadipyl-phosphate reductase; Orff
- EC
- 1.2.1.-, 1.2.1.38
- UniProt
- O50146, Q9ZND7
- Ligands
- NAP, ZN
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyl-gamma-glutamyl-PHOSPHATE/N-acetyl-gamma- aminoadipyl-phosphate reductase (EC 1.2.1.-, 1.2.1.38) | protein | 344 | 33% helix, 22% strand | O50146 |
| B | N-acetyl-gamma-glutamyl-PHOSPHATE/N-acetyl-gamma- aminoadipyl-phosphate reductase (EC 1.2.1.-, 1.2.1.38) | protein | 342 | 33% helix, 23% strand | O50146 |
| C | Orff | protein | 46 | 0% helix, 41% strand | Q9ZND7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains C
- ACY · Acetic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.70 | 0.78 | 49 | NAP |
| 2 | 540 | 0.68 | 0.78 | 48 | NAP |
| 3 | 258 | 0.55 | 0.77 | 49 | empty |
| 4 | 118 | 0.42 | 0.76 | 23 | empty |
| 5 | 66 | 0.32 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1965 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5EIO · Crystal structure of LysY from Thermus thermophilus complexed with NADP+ and… · the same entry in another collection · chain A against A, TM-score 1.00
- O50146 · AlphaFold monomer V2.0 prediction for [lysw]-L-2-aminoadipate 6-phosphate reductase… · a predicted model of the same protein · 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 O50146
- Every structure of UniProt Q9ZND7
- Elsewhere: RCSB PDB 5EIO · PDBe 5EIO · UniProt O50146 · UniProt Q9ZND7
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