- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.51 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)
DGJ.6: 13 residues within 4Å:- Chain A: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, Y.175, R.196, D.200
- Ligands: GOL.11, GOL.12
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:D.62, A:D.62, A:K.137, A:K.137, A:R.196, A:R.196
- Water bridges: A:D.139, A:Y.175, A:D.200, A:D.235
DGJ.17: 13 residues within 4Å:- Chain B: W.16, D.61, D.62, Y.102, C.110, M.111, K.137, D.139, Y.175, R.196, D.200
- Ligands: GOL.20, GOL.22
11 PLIP interactions:11 interactions with chain B- Hydrogen bonds: B:D.62, B:D.62, B:Y.102, B:K.137, B:K.137, B:R.196, B:R.196
- Water bridges: B:D.139, B:Y.175, B:D.200, B:D.235
- 2 x CIT: CITRIC ACID(Non-functional Binders)
CIT.7: 7 residues within 4Å:- Chain A: I.23, N.24, C.25, D.26, D.77, K.79, R.80
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:K.79
- Hydrogen bonds: A:I.23, A:C.25, A:D.26, A:D.26
- Water bridges: A:D.77, A:D.77, A:K.79, A:K.79
- Salt bridges: A:K.79, A:R.80
CIT.18: 7 residues within 4Å:- Chain B: I.23, N.24, C.25, D.26, D.77, K.79, R.80
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:K.79
- Hydrogen bonds: B:C.25, B:D.26, B:D.26, B:D.26
- Water bridges: B:N.24, B:K.79, B:R.80
- Salt bridges: B:R.80
- 14 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 4 residues within 4Å:- Chain A: N.31, D.268, R.270, T.271
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.31, A:D.268, A:D.268
GOL.9: 9 residues within 4Å:- Chain A: L.6, T.8, P.9, P.10, M.11, G.54, T.56, Y.57, Q.290
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:T.8, A:M.11, A:M.11, A:T.56
- Water bridges: A:L.6, A:T.8, A:T.56, A:Y.57
GOL.10: 3 residues within 4Å:- Chain A: M.111, G.112, Y.113
1 PLIP interactions:1 interactions with chain A- Water bridges: A:Y.113
GOL.11: 6 residues within 4Å:- Chain A: W.16, C.110, M.111, D.200
- Ligands: DGJ.6, GOL.12
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.200
- Water bridges: A:Q.202, A:Q.202
GOL.12: 6 residues within 4Å:- Chain A: A.174, Y.175, D.199, D.200
- Ligands: DGJ.6, GOL.11
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.199, A:D.199, A:D.200
- Water bridges: A:D.200
GOL.13: 6 residues within 4Å:- Chain A: L.306, R.327, T.328, D.329
- Chain B: R.20, Q.202
7 PLIP interactions:3 interactions with chain B, 4 interactions with chain A- Hydrogen bonds: B:R.20, B:Q.202, A:T.328, A:T.328
- Water bridges: B:Q.202, A:C.326, A:T.328
GOL.14: 7 residues within 4Å:- Chain A: L.209, L.212, N.213, V.216, E.308, Y.310, C.326
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:L.209, A:Y.310, A:Y.310
GOL.15: 7 residues within 4Å:- Chain A: P.29, C.32, S.34, E.35, Q.36, K.79, R.80
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:P.29, A:S.34, A:Q.36, A:K.79
- Water bridges: A:E.35, A:Q.36
GOL.19: 6 residues within 4Å:- Chain B: L.209, N.213, V.216, E.308, Y.310, C.326
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:L.209, B:Y.310, B:Y.310
- Water bridges: B:R.299
GOL.20: 6 residues within 4Å:- Chain B: W.16, C.110, M.111, D.200
- Ligands: DGJ.17, GOL.22
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.200
- Water bridges: B:Q.202, B:Q.202
GOL.21: 3 residues within 4Å:- Chain B: M.111, G.112, Y.113
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:M.111
GOL.22: 6 residues within 4Å:- Chain B: A.174, Y.175, D.199, D.200
- Ligands: DGJ.17, GOL.20
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.199, B:D.199, B:D.200
- Water bridges: B:D.200
GOL.23: 6 residues within 4Å:- Chain A: R.20, Q.202
- Chain B: L.306, R.327, T.328, D.329
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:T.328, B:T.328, A:R.20, A:R.20, A:Q.202
GOL.24: 9 residues within 4Å:- Chain B: L.6, T.8, P.9, P.10, M.11, G.54, T.56, Y.57, Q.290
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:T.8, B:T.8, B:M.11, B:M.11, B:T.56
- Water bridges: B:L.6, B:Q.7
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Clark, N.E. et al., Pharmacological chaperones for human alpha-N-acetylgalactosaminidase. Proc.Natl.Acad.Sci.USA (2012)
- Release Date
- 2012-10-10
- Peptides
- Alpha-N-acetylgalactosaminidase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.51 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)
- 2 x CIT: CITRIC ACID(Non-functional Binders)
- 14 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Clark, N.E. et al., Pharmacological chaperones for human alpha-N-acetylgalactosaminidase. Proc.Natl.Acad.Sci.USA (2012)
- Release Date
- 2012-10-10
- Peptides
- Alpha-N-acetylgalactosaminidase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B