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Crystal structure of pnpb complex with FMN
Analyse Crystal structure of pnpb complex with FMN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LAF
- Type
- protein
- Length
- 793 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(P)H dehydrogenase (quinone)
- EC
- 1.6.5.2
- UniProt
- C1I202
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 207 | 41% helix, 20% strand | C1I202 |
| B | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 205 | 40% helix, 19% strand | C1I202 |
| C | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 193 | 37% helix, 21% strand | C1I202 |
| D | NAD(P)H dehydrogenase (quinone) (EC 1.6.5.2) | protein | 188 | 36% helix, 22% strand | C1I202 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.83 | 0.98 | 29 | empty |
| 2 | 473 | 0.68 | 0.79 | 45 | FMN |
| 3 | 492 | 0.68 | 0.79 | 41 | FMN |
| 4 | 323 | 0.64 | 0.79 | 34 | FMN |
| 5 | 306 | 0.62 | 0.79 | 28 | FMN |
Interfaces
6 interfaces between chains.
- A–B · 1138 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1099 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 988 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 982 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 926 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 C1I202
- Elsewhere: RCSB PDB 4LAF · PDBe 4LAF · UniProt C1I202
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