Research workbench
Structure of a human glycosylphosphatidylinositol (gpi) transamidase
Analyse Structure of a human glycosylphosphatidylinositol (gpi) transamidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W72
- Type
- protein
- Length
- 2,398 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol glycan anchor biosynthesis class U protein; Gpi transamidase…
- EC
- 3.-.-.-
- UniProt
- Q9H490, Q96S52, Q969N2, Q92643, O43292
- Ligands
- 8JY, NAG, BMA, CA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Phosphatidylinositol glycan anchor biosynthesis class U protein | protein | 420 | 71% helix, 0% strand | Q9H490 |
| S | Gpi transamidase component pig-S | protein | 533 | 40% helix, 17% strand | Q96S52 |
| T | Gpi transamidase component pig-T | protein | 527 | 17% helix, 34% strand | Q969N2 |
| K | Gpi-anchor transamidase (EC 3.-.-.-) | protein | 330 | 26% helix, 15% strand | Q92643 |
| A | Glycosylphosphatidylinositol anchor attachment 1 protein | protein | 588 | 55% helix, 11% strand | O43292 |
Ligands and binding sites
- 8JY · [2-[[(2~{R})-2-hexanoyloxy-3-[(~{E})-hex-3-enoxy]propoxy]-oxidanyl-phosphoryl]oxy-3,4,5,6-tetrakis(oxidanyl)phenyl] (2~{E},4~{E})-hepta-2,4-dienoate · ligand · chains U, T
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, S, T
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · chains K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.87 | 0.88 | 127 | empty |
| 2 | 861 | 0.86 | 0.87 | 123 | empty |
| 3 | 208 | 0.83 | 0.96 | 31 | empty |
| 4 | 330 | 0.79 | 0.89 | 32 | empty |
| 5 | 131 | 0.78 | 0.96 | 30 | empty |
Interfaces
9 interfaces between chains.
- S–K · 2632 Ų buried · 26 hydrogen bonds · protein-protein
- U–T · 2470 Ų buried · 22 hydrogen bonds · protein-protein
- T–K · 2330 Ų buried · 35 hydrogen bonds · protein-protein
- T–A · 1527 Ų buried · 15 hydrogen bonds · protein-protein
- S–T · 1485 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 7W72 · Structure of a human glycosylphosphatidylinositol (GPI) transamidase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H490 · AlphaFold monomer V2.0 prediction for phosphatidylinositol glycan anchor biosynthesis… · a predicted model of the same protein · chain U against A, TM-score 0.99
- O43292 · AlphaFold monomer V2.0 prediction for glycosylphosphatidylinositol anchor attachment 1… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q969N2 · AlphaFold monomer V2.0 prediction for gpi transamidase component pig-T (Q969N2) · a predicted model of the same protein · chain T against A, TM-score 0.92
- Q96S52 · AlphaFold monomer V2.0 prediction for gpi transamidase component pig-S (Q96S52) · a predicted model of the same protein · chain S against A, TM-score 0.90
- Q92643 · AlphaFold monomer V2.0 prediction for gpi-anchor transamidase (Q92643) · a predicted model of the same protein · chain K against A, TM-score 0.81
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 Q9H490
- Every structure of UniProt Q96S52
- Every structure of UniProt Q969N2
- Every structure of UniProt Q92643
- Every structure of UniProt O43292
- Elsewhere: RCSB PDB 7W72 · PDBe 7W72 · UniProt Q9H490 · UniProt Q96S52 · UniProt Q969N2 · UniProt Q92643 · UniProt O43292
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