- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-mer
- Ligands
- 1 x MET- SER- SER: Met-Ser-Ser peptide(Non-covalent)
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 13 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 4 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)
6OU.6: 23 residues within 4Å:- Chain B: T.120, L.297, A.300, S.301, R.303, Y.474, L.522, L.526, P.555, T.558, L.559, S.562, L.563, W.566, L.582, A.585, A.586, L.587, Q.589, G.590, L.601, F.602, L.605
17 PLIP interactions:17 interactions with chain B- Hydrophobic interactions: B:A.300, B:Y.474, B:L.522, B:L.526, B:T.558, B:L.559, B:L.559, B:L.559, B:L.563, B:L.563, B:W.566, B:W.566, B:F.602, B:L.605, B:L.605
- Hydrogen bonds: B:R.303
- Salt bridges: B:R.303
6OU.7: 15 residues within 4Å:- Chain B: F.359, S.372, I.373, G.374, M.377, L.384, A.509, G.513, L.517
- Chain F: V.366, L.370, F.388
- Ligands: Y01.3, AJP.15, 81Q.31
7 PLIP interactions:6 interactions with chain B, 1 interactions with chain F- Hydrophobic interactions: B:L.384, B:A.509, B:L.517, B:L.517, F:L.370
- Hydrogen bonds: B:S.372, B:G.374
6OU.8: 11 residues within 4Å:- Chain B: R.313, Y.507, Q.511, C.514, L.600, L.604
- Chain E: Y.363
- Chain F: F.29, L.369, P.372, H.376
5 PLIP interactions:4 interactions with chain F, 1 interactions with chain B- Hydrophobic interactions: F:L.369, F:L.369, B:L.600
- Salt bridges: F:H.376, F:H.376
6OU.20: 18 residues within 4Å:- Chain B: W.395, L.433, I.506
- Chain F: F.145, N.149, P.150, Y.151, F.344, N.348, Y.351, F.358, T.361, I.364, I.365, S.368, Y.407
- Ligands: Y01.5, Y01.25
11 PLIP interactions:8 interactions with chain F, 3 interactions with chain B- Hydrophobic interactions: F:P.150, F:Y.151, F:F.358, F:F.358, F:I.364, F:I.365, B:L.433, B:I.506, B:I.506
- Hydrogen bonds: F:N.348, F:N.348
- 1 x AJP: Digitonin(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)
LBN.18: 24 residues within 4Å:- Chain D: A.29, I.30, G.33, L.34, W.37, W.38, T.41, E.42, D.517, K.520, F.521, Y.524, I.525, F.528, M.531, A.532, I.535, L.536
- Chain E: V.538
- Chain F: F.290, V.294, I.297, N.298, F.301
19 PLIP interactions:14 interactions with chain D, 4 interactions with chain F, 1 interactions with chain E- Hydrophobic interactions: D:I.30, D:W.37, D:W.37, D:W.37, D:F.521, D:Y.524, D:I.525, D:F.528, D:F.528, D:A.532, D:I.535, D:L.536, F:F.290, F:I.297, F:N.298, F:F.301, E:V.538
- Hydrogen bonds: D:D.517
- pi-Cation interactions: D:W.38
- 1 x 80T: [(2R)-1-hexadecanoyloxy-3-[[3-[[(2R)-3-hexadecanoyloxy-2-[(Z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (Z)-octadec-9-enoate(Non-covalent)
80T.21: 19 residues within 4Å:- Chain D: L.13, R.17, R.20, L.23, F.24, A.27, V.28
- Chain F: F.202, L.206, L.207, V.217, K.218, M.219, F.224, W.225, S.228, W.229, A.307, K.311
19 PLIP interactions:10 interactions with chain D, 9 interactions with chain F- Hydrophobic interactions: D:L.23, D:L.23, D:F.24, D:A.27, D:V.28, F:F.202, F:L.206, F:L.207, F:W.225, F:W.229, F:K.311
- Hydrogen bonds: D:R.20, F:M.219
- Salt bridges: D:R.17, D:R.20, D:R.20, D:R.20, F:K.218, F:K.311
- 2 x 80Y: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate(Non-covalent)
80Y.27: 7 residues within 4Å:- Chain A: G.299, T.300, T.301
- Ligands: MET-SER-SER.1, MET-SER-SER.1, 80Y.29, 05E.30
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:G.299, A:G.299, A:T.301, A:T.301
80Y.29: 9 residues within 4Å:- Chain A: T.301
- Chain B: Y.51, S.53, Q.357, S.358, F.359
- Ligands: 80Y.27, PA1.28, 05E.30
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.51, B:S.53, B:Q.357, B:S.358
- 1 x PA1: 2-amino-2-deoxy-alpha-D-glucopyranose(Non-covalent)
- 1 x 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(Non-covalent)
- 1 x 81Q: [(2R)-1-[[(1S,2R,3R,4S,5S,6R)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)
81Q.31: 16 residues within 4Å:- Chain A: L.310
- Chain E: D.523, S.525, M.526, N.529
- Chain F: V.359, C.362, I.363, V.366, N.387, F.388, A.391, T.395
- Ligands: Y01.3, 6OU.7, PA1.28
7 PLIP interactions:3 interactions with chain F, 2 interactions with chain E, 2 interactions with chain A- Hydrophobic interactions: F:V.359, F:V.366, A:L.310, A:L.310
- Hydrogen bonds: F:N.387, E:S.525, E:N.529
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Xu, Y. et al., Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis. Nat Commun (2023)
- Release Date
- 2023-08-16
- Peptides
- UL16-binding protein 2,GFP-like fluorescent chromoprotein cFP484: A
Glycosylphosphatidylinositol anchor attachment 1 protein,GFP-like fluorescent chromoprotein cFP484: B
GPI-anchor transamidase,GFP-like fluorescent chromoprotein cFP484: C
GPI transamidase component PIG-S,GFP-like fluorescent chromoprotein cFP484: D
GPI transamidase component PIG-T,GFP-like fluorescent chromoprotein cFP484: E
Phosphatidylinositol glycan anchor biosynthesis class U protein,GFP-like fluorescent chromoprotein cFP484: F - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
GC
KD
SE
TF
U - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-mer
- Ligands
- 1 x MET- SER- SER: Met-Ser-Ser peptide(Non-covalent)
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 13 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 4 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)
- 1 x AJP: Digitonin(Non-covalent)
- 1 x CA: CALCIUM ION(Non-covalent)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)
- 1 x 80T: [(2R)-1-hexadecanoyloxy-3-[[3-[[(2R)-3-hexadecanoyloxy-2-[(Z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (Z)-octadec-9-enoate(Non-covalent)
- 2 x 80Y: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate(Non-covalent)
- 1 x PA1: 2-amino-2-deoxy-alpha-D-glucopyranose(Non-covalent)
- 1 x 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(Non-covalent)
- 1 x 81Q: [(2R)-1-[[(1S,2R,3R,4S,5S,6R)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Xu, Y. et al., Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis. Nat Commun (2023)
- Release Date
- 2023-08-16
- Peptides
- UL16-binding protein 2,GFP-like fluorescent chromoprotein cFP484: A
Glycosylphosphatidylinositol anchor attachment 1 protein,GFP-like fluorescent chromoprotein cFP484: B
GPI-anchor transamidase,GFP-like fluorescent chromoprotein cFP484: C
GPI transamidase component PIG-S,GFP-like fluorescent chromoprotein cFP484: D
GPI transamidase component PIG-T,GFP-like fluorescent chromoprotein cFP484: E
Phosphatidylinositol glycan anchor biosynthesis class U protein,GFP-like fluorescent chromoprotein cFP484: F - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
GC
KD
SE
TF
U - Membrane
-
We predict this structure to be a membrane protein.