MolNFT v1 · #117785 · protein
Crystal structure of C148A mutant of lysy from thermus thermophilus in complex with NADP+ and lysw-gamma-aminoadipic acid
5EIN · N-acetyl-gamma-glutamyl-PHOSPHATE/N-acetyl-gamma…: “Crystal structure of C148A mutant of lysy from thermus thermophilus in complex with NADP+ and…”. X-ray diffraction, 3 ligands (NAP, UN1, ZN), 5 pockets (best druggability 0.76).…
- PDB
- 5EIN
- Type
- protein
- Length
- 740 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, UN1, ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 23% 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 | 32% helix, 22% strand | O50146 |
| C | Orff | protein | 54 | 0% helix, 35% strand | Q9ZND7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- UN1 · 2-aminohexanedioic acid · ligand · chains A, C
- ZN · Zinc ion · metal · chains C
- FMT · Formic acid · additive · 23 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.76 | 0.79 | 95 | NAP, FMT, UN1 |
| 2 | 729 | 0.74 | 0.80 | 71 | NAP, FMT |
| 3 | 89 | 0.35 | 0.75 | 20 | empty |
| 4 | 67 | 0.29 | 0.74 | 18 | FMT |
| 5 | 58 | 0.28 | 0.74 | 14 | FMT |
Interfaces
3 interfaces between chains.
- A–B · 1962 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 554 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 390 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5EIN · Crystal structure of C148A mutant of LysY from Thermus thermophilus in complex with NADP+… · 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 5EIN · PDBe 5EIN · UniProt O50146 · UniProt Q9ZND7
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