MolNFT v1 · #105066 · protein
Crystal structure of the vitamin B3 transporter pnuc
4QTN · Nicotinamide riboside transporter pnuc: “Crystal structure of the vitamin B3 transporter pnuc”. X-ray diffraction, 1 ligand (NNR), 16 pockets (best druggability 0.82). MolNFT v1 #105066 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QTN
- Type
- protein
- Length
- 707 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicotinamide riboside transporter pnuc
- UniProt
- D2ZZC1
- Ligands
- NNR
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nicotinamide riboside transporter pnuc | protein | 235 | 78% helix, 3% strand | D2ZZC1 |
| C | Nicotinamide riboside transporter pnuc | protein | 237 | 71% helix, 1% strand | D2ZZC1 |
Ligands and binding sites
- NNR · Nicotinamide riboside · ligand · 3 copies · chains A, B, C
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.82 | 0.99 | 28 | NNR |
| 2 | 135 | 0.82 | 0.98 | 30 | NNR |
| 3 | 139 | 0.81 | 0.98 | 30 | NNR |
| 4 | 695 | 0.80 | 0.84 | 66 | empty |
| 5 | 109 | 0.62 | 0.86 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1103 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1055 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 1047 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4QTN · Crystal structure of the Vitamin B3 transporter PnuC · the same entry in another collection · chain A against A, TM-score 1.00
- D2ZZC1 · AlphaFold monomer V2.0 prediction for nicotinamide riboside transporter pnuc (D2ZZC1) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 D2ZZC1
- Elsewhere: RCSB PDB 4QTN · PDBe 4QTN · UniProt D2ZZC1
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