MolNFT v1 · #190177 · protein
Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 ångström resolution
7WLD · Glycosylphosphatidylinositol anchor attachment 1 protein: “Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 ångström resolution”. Electron microscopy, 13 ligands (Y01, CLR, BJR), 20 pockets…
- PDB
- 7WLD
- Type
- protein
- Length
- 2,393 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosylphosphatidylinositol anchor attachment 1 protein; Gpi-anchor transamidase; Gpi…
- EC
- 3.-.-.-
- UniProt
- O43292, Q92643, Q96S52, Q969N2, Q9H490
- Ligands
- Y01, CLR, BJR, AJP, PEE, P5S, 05E, PA1, CDL, DKB, 06O, NAG, CA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Glycosylphosphatidylinositol anchor attachment 1 protein | protein | 583 | 55% helix, 14% strand | O43292 |
| K | Gpi-anchor transamidase (EC 3.-.-.-) | protein | 331 | 28% helix, 17% strand | Q92643 |
| S | Gpi transamidase component pig-S | protein | 532 | 42% helix, 20% strand | Q96S52 |
| T | Gpi transamidase component pig-T | protein | 528 | 16% helix, 37% strand | Q969N2 |
| U | Phosphatidylinositol glycan anchor biosynthesis class U protein | protein | 419 | 73% helix, 0% strand | Q9H490 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 9 copies · chains G, U
- CLR · Cholesterol · ligand · 5 copies · chains S, U, K
- BJR · (4S,7R)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-3,5,8-trioxa-4lambda~5~-phosphahexacosan-1-aminium · ligand · 2 copies · chains G, U
- AJP · Digitonin · ligand · chains G
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · chains G
- P5S · O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy) propyl]oxy}(hydroxy)phosphoryl]-L-serine · ligand · chains K, U
- 05E · 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate · ligand · chains G, T
- PA1 · 2-amino-2-deoxy-alpha-D-glucopyranose · ligand · chains T, U
- CDL · Cardiolipin · ligand · chains S, U
- DKB · [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate · ligand · chains G, U
- 06O · [(2~{R})-1-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R}, 4~{S},5~{S},6~{R})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propan-2-yl] (9~{Z},11~{Z})-octadeca-9, 11-dienoate · ligand · chains T, U
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains G, S, T
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.88 | 0.89 | 124 | empty |
| 2 | 1005 | 0.87 | 0.88 | 105 | PEE |
| 3 | 1008 | 0.86 | 0.87 | 79 | empty |
| 4 | 1127 | 0.85 | 0.86 | 138 | empty |
| 5 | 366 | 0.84 | 0.93 | 63 | empty |
Interfaces
9 interfaces between chains.
- T–U · 2468 Ų buried · 17 hydrogen bonds · protein-protein
- K–S · 2436 Ų buried · 24 hydrogen bonds · protein-protein
- K–T · 2085 Ų buried · 25 hydrogen bonds · protein-protein
- S–T · 1444 Ų buried · 8 hydrogen bonds · protein-protein
- G–T · 1411 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7WLD · Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53… · the same entry in another collection · chain U against U, 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 0.98
- O43292 · AlphaFold monomer V2.0 prediction for glycosylphosphatidylinositol anchor attachment 1… · a predicted model of the same protein · chain G against A, TM-score 0.97
- 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 0.88
- 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 O43292
- Every structure of UniProt Q92643
- Every structure of UniProt Q96S52
- Every structure of UniProt Q969N2
- Every structure of UniProt Q9H490
- Elsewhere: RCSB PDB 7WLD · PDBe 7WLD · UniProt O43292 · UniProt Q92643 · UniProt Q96S52 · UniProt Q969N2 · UniProt Q9H490
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