MolNFT v1 · #152489 · protein
Crystal structure of arabidopsis thaliana UGT89C1 complexed with udp
6IJ9 · Udp-glycosyltransferase 89C1: “Crystal structure of arabidopsis thaliana UGT89C1 complexed with udp”. X-ray diffraction, 1 ligand (UDP), 19 pockets (best druggability 0.90). MolNFT v1 #152489 on GenesisL1: 3D structure, binding…
- PDB
- 6IJ9
- Type
- protein
- Length
- 1,619 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glycosyltransferase 89C1
- EC
- 2.4.1.-
- UniProt
- Q9LNE6
- Ligands
- UDP
- Pockets
- 19 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 410 | 45% helix, 14% strand | Q9LNE6 |
| B | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 408 | 45% helix, 14% strand | Q9LNE6 |
| C | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 413 | 46% helix, 14% strand | Q9LNE6 |
| D | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 388 | 47% helix, 14% strand | Q9LNE6 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.90 | 0.91 | 160 | UDP |
| 2 | 1188 | 0.88 | 0.89 | 146 | UDP |
| 3 | 82 | 0.71 | 0.94 | 21 | empty |
| 4 | 914 | 0.71 | 0.76 | 58 | empty |
| 5 | 526 | 0.66 | 0.77 | 41 | empty |
Interfaces
4 interfaces between chains.
- B–D · 943 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 938 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 363 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6IJ9 · Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP · the same entry in another collection · chain D against D, TM-score 1.00
- Q9LNE6 · AlphaFold monomer V2.0 prediction for flavonol 7-O-rhamnosyltransferase (Q9LNE6) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9LNE6
- Elsewhere: RCSB PDB 6IJ9 · PDBe 6IJ9 · UniProt Q9LNE6
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