Research workbench
An unprecedented NADPH domain conformation in lysine monooxygenase nbtg from nocardia farcinica
Analyse An unprecedented NADPH domain conformation in lysine monooxygenase nbtg from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D7E
- Type
- protein
- Length
- 1,465 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lys monooxygenase
- UniProt
- Q5Z1T5
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lys monooxygenase | protein | 396 | 37% helix, 23% strand | Q5Z1T5 |
| B | L-lys monooxygenase | protein | 392 | 37% helix, 21% strand | Q5Z1T5 |
| C | L-lys monooxygenase | protein | 377 | 38% helix, 22% strand | Q5Z1T5 |
| D | L-lys monooxygenase | protein | 300 | 41% helix, 14% strand | Q5Z1T5 |
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
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.82 | 0.83 | 90 | FAD |
| 2 | 1130 | 0.82 | 0.83 | 86 | FAD |
| 3 | 997 | 0.78 | 0.80 | 92 | empty |
| 4 | 976 | 0.77 | 0.79 | 86 | FAD |
| 5 | 798 | 0.77 | 0.81 | 70 | FAD |
Interfaces
5 interfaces between chains.
- B–D · 1391 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1338 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 924 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 451 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4D7E · An unprecedented NADPH domain conformation in Lysine Monooxygenase NbtG from Nocardia… · 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 Q5Z1T5
- Elsewhere: RCSB PDB 4D7E · PDBe 4D7E · UniProt Q5Z1T5
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