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Crystal structure of human glcat-P in complex with N- acetyllactosamine, udp, and MN2+
Analyse Crystal structure of human glcat-P in complex with N- acetyllactosamine, udp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V84
- Type
- protein
- Length
- 488 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, GAL, NDG, NAG, MN
- Pockets
- 4 · best druggability 0.66
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 | 31% helix, 22% strand | Q9P2W7 |
| B | Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 1 (EC 2.4.1.135) | protein | 243 | 29% helix, 22% strand | Q9P2W7 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 | 446 | 0.66 | 0.78 | 56 | GAL, MN, UDP |
| 2 | 451 | 0.66 | 0.78 | 48 | GAL, MN, UDP |
| 3 | 180 | 0.54 | 0.79 | 21 | empty |
| 4 | 204 | 0.54 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2109 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1V84 · Crystal structure of human GlcAT-P in complex with N-acetyllactosamine, 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 A 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 1V84 · PDBe 1V84 · UniProt Q9P2W7
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