Research workbench
Crystal structure of arabidopsis thaliana UGT89C1 complexed with udp- L-rhamnose
Analyse Crystal structure of arabidopsis thaliana UGT89C1 complexed with udp- L-rhamnose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IJA
- Type
- protein
- Length
- 1,603 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
- AWU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 415 | 43% helix, 14% strand | Q9LNE6 |
| B | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 413 | 42% helix, 15% strand | Q9LNE6 |
| C | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 386 | 41% helix, 12% strand | Q9LNE6 |
| D | Udp-glycosyltransferase 89C1 (EC 2.4.1.-) | protein | 389 | 43% helix, 14% strand | Q9LNE6 |
Ligands and binding sites
- AWU · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene) pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.87 | 0.88 | 135 | AWU |
| 2 | 580 | 0.81 | 0.87 | 74 | AWU |
| 3 | 805 | 0.78 | 0.81 | 86 | empty |
| 4 | 784 | 0.76 | 0.80 | 63 | empty |
| 5 | 333 | 0.76 | 0.87 | 52 | empty |
Interfaces
4 interfaces between chains.
- A–D · 787 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6IJA · Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP-L-rhamnose · 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 0.98
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 6IJA · PDBe 6IJA · UniProt Q9LNE6
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