MolNFT v1 · #101618 · protein
Structure of bacterial type II NADH dehydrogenase from caldalkalibacillus thermarum at 2.5A resolution
4NWZ · FAD-dependent pyridine nucleotide-disulfide oxidoreductase: “Structure of bacterial type II NADH dehydrogenase from caldalkalibacillus thermarum at 2.5A resolution”. X-ray diffraction, 1 ligand (FAD), 15 pockets (best druggability…
- PDB
- 4NWZ
- Type
- protein
- Length
- 1,557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent pyridine nucleotide-disulfide oxidoreductase
- UniProt
- F5L3B8
- Ligands
- FAD
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 395 | 35% helix, 27% strand | F5L3B8 |
| C | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 394 | 35% helix, 27% strand | F5L3B8 |
| D | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | protein | 373 | 37% helix, 23% strand | F5L3B8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.82 | 0.83 | 115 | FAD |
| 2 | 903 | 0.82 | 0.84 | 88 | FAD |
| 3 | 429 | 0.80 | 0.88 | 67 | empty |
| 4 | 435 | 0.80 | 0.88 | 52 | FAD |
| 5 | 403 | 0.78 | 0.87 | 57 | FAD |
Interfaces
5 interfaces between chains.
- B–C · 660 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 354 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 279 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 215 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 202 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NWZ · Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at… · the same entry in another collection · chain D against D, 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 F5L3B8
- Elsewhere: RCSB PDB 4NWZ · PDBe 4NWZ · UniProt F5L3B8
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