Research workbench
Crystal structure of B. pseudomallei fabi in complex with NAD and PT405
Analyse Crystal structure of B. pseudomallei fabi in complex with NAD and PT405 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I7F
- Type
- protein
- Length
- 3,084 residues
- Chains
- 12
- 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
- A0A069B9A4
- Ligands
- NAD, 68O
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E, H, C, A, F, G, D, I, K, L, J | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 257 | 46% helix, 17% strand | A0A069B9A4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains B, E, H, C, A, F, G, D, I, K, L, J
- 68O · 5-ethyl-4-fluoro-2-(2-fluorophenoxy)phenol · ligand · 12 copies · chains B, E, H, C, A, F, G, D, I, K, L, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.86 | 0.87 | 99 | NAD, 68O |
| 2 | 550 | 0.85 | 0.90 | 62 | NAD, 68O |
| 3 | 1147 | 0.84 | 0.86 | 52 | empty |
| 4 | 1149 | 0.84 | 0.86 | 54 | empty |
| 5 | 1144 | 0.84 | 0.85 | 53 | empty |
Interfaces
25 interfaces between chains.
- I–L · 1671 Ų buried · 35 hydrogen bonds · protein-protein
- K–J · 1657 Ų buried · 35 hydrogen bonds · protein-protein
- F–D · 1646 Ų buried · 33 hydrogen bonds · protein-protein
- A–G · 1646 Ų buried · 36 hydrogen bonds · protein-protein
- E–C · 1642 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5I7F · Crystal structure of B. pseudomallei FabI in complex with NAD and PT405 · the same entry in another collection · chain B against B, 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 A0A069B9A4
- Elsewhere: RCSB PDB 5I7F · PDBe 5I7F · UniProt A0A069B9A4
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