Research workbench
How nature bridges the gap: crystallographic elucidation of pyridomycin binding to inha
Analyse How nature bridges the gap: crystallographic elucidation of pyridomycin binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BII
- Type
- protein
- Length
- 1,027 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
- P0A5Y6
- Ligands
- NAD, PYW
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 260 | 45% helix, 17% strand | P0A5Y6 |
| B | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 255 | 45% helix, 17% strand | P0A5Y6 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 249 | 44% helix, 18% strand | P0A5Y6 |
| D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 263 | 45% helix, 17% strand | P0A5Y6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- PYW · Pyridomycin · ligand · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.83 | 0.84 | 55 | empty |
| 2 | 736 | 0.77 | 0.81 | 53 | PYW |
| 3 | 564 | 0.72 | 0.80 | 50 | NAD, PYW |
| 4 | 494 | 0.70 | 0.79 | 43 | NAD, PYW |
| 5 | 459 | 0.68 | 0.79 | 49 | NAD |
Interfaces
6 interfaces between chains.
- B–D · 1574 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1569 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1492 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1436 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 688 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4BII · How nature bridges the gap: Crystallographic elucidation of pyridomycin binding to InhA · the same entry in another collection · 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 P0A5Y6
- Elsewhere: RCSB PDB 4BII · PDBe 4BII · UniProt P0A5Y6
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