Research workbench
Crystal structure of fabi-NADH complex from alistipes finegoldii
Analyse Crystal structure of fabi-NADH complex from alistipes finegoldii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VLY
- Type
- protein
- Length
- 1,144 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
- A0A174E195
- Ligands
- NAI, CL
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 293 | 44% helix, 16% strand | A0A174E195 |
| B, D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 284 | 46% helix, 17% strand | A0A174E195 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 283 | 47% helix, 17% strand | A0A174E195 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.84 | 0.85 | 56 | empty |
| 2 | 557 | 0.81 | 0.87 | 64 | GOL, NAI |
| 3 | 473 | 0.80 | 0.87 | 45 | NAI |
| 4 | 439 | 0.79 | 0.87 | 46 | GOL, NAI |
| 5 | 481 | 0.77 | 0.85 | 46 | NAI |
Interfaces
6 interfaces between chains.
- A–D · 2555 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2399 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1623 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1610 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1495 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6VLY · Crystal structure of FabI-NADH complex from Alistipes finegoldii · 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 A0A174E195
- Elsewhere: RCSB PDB 6VLY · PDBe 6VLY · UniProt A0A174E195
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