Research workbench
Crystal structure of inha in complex with 3-nitropropanoic acid inhibitor
Analyse Crystal structure of inha in complex with 3-nitropropanoic acid inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E48
- Type
- protein
- Length
- 1,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADH]
- EC
- 1.3.1.9
- UniProt
- P9WGR1
- Ligands
- NAD, 3NP
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 267 | 47% helix, 16% strand | P9WGR1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 3NP · 3-nitropropanoic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.84 | 0.85 | 56 | empty |
| 2 | 655 | 0.81 | 0.85 | 53 | NAD, 3NP |
| 3 | 663 | 0.80 | 0.84 | 56 | NAD, 3NP |
| 4 | 621 | 0.80 | 0.84 | 52 | NAD, 3NP |
| 5 | 634 | 0.79 | 0.84 | 53 | NAD, 3NP |
Interfaces
6 interfaces between chains.
- B–C · 1574 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1574 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1477 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1473 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 647 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7E48 · Crystal structure of InhA in complex with 3-nitropropanoic acid inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P9WGR1 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH]… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P9WGR1
- Elsewhere: RCSB PDB 7E48 · PDBe 7E48 · UniProt P9WGR1
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