MolNFT v1 · #24845 · protein
Crystal structure of human glcat-P in complex with udp and MN2+
1V83 · Galactosylgalactosylxylosylprotein 3-beta…: “Crystal structure of human glcat-P in complex with udp and MN2+”. X-ray diffraction, 2 ligands (UDP, MN), 4 pockets (best druggability 0.65). MolNFT v1 #24845 on GenesisL1: 3D structure…
- PDB
- 1V83
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 1
- EC
- 2.4.1.135
- UniProt
- Q9P2W7
- Ligands
- UDP, MN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 1 (EC 2.4.1.135) | protein | 245 | 30% helix, 22% strand | Q9P2W7 |
| B | Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 1 (EC 2.4.1.135) | protein | 241 | 30% helix, 22% strand | Q9P2W7 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.65 | 0.78 | 46 | MN, UDP |
| 2 | 449 | 0.63 | 0.77 | 47 | MN, UDP |
| 3 | 207 | 0.54 | 0.78 | 22 | empty |
| 4 | 174 | 0.53 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2090 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1V83 · Crystal structure of human GlcAT-P in complex with Udp and Mn2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P2W7 · AlphaFold monomer V2.0 prediction for galactosylgalactosylxylosylprotein… · a predicted model of the same protein · chain B 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 Q9P2W7
- Elsewhere: RCSB PDB 1V83 · PDBe 1V83 · UniProt Q9P2W7
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