- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.76 Å
- Oligo State
- hetero-5-1-mer
- Ligands
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- 6 x BMA: beta-D-mannopyranose(Non-covalent)
BMA.2: 10 residues within 4Å:- Chain A: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324
- Chain C: C.257
- Ligands: PO4.1, NDG.3
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:R.79, A:D.124, A:Y.262, A:D.324
- Water bridges: A:R.79, A:D.124, A:H.194, A:K.232
- Salt bridges: A:K.232
BMA.8: 10 residues within 4Å:- Chain A: C.257
- Chain B: F.63, N.64, R.79, Y.262, V.301, F.303, D.324
- Ligands: PO4.7, NDG.9
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:R.79
- Water bridges: B:R.170, B:H.194, B:K.232, B:Y.262, B:D.324, B:D.324
- Salt bridges: B:R.170, B:K.232
BMA.13: 10 residues within 4Å:- Chain B: C.257
- Chain C: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324
- Ligands: PO4.12, NDG.14
8 PLIP interactions:8 interactions with chain C- Hydrogen bonds: C:R.79, C:D.124, C:Y.262, C:D.324
- Water bridges: C:R.79, C:D.124, C:H.194, C:K.232
BMA.18: 10 residues within 4Å:- Chain D: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324
- Chain F: C.257
- Ligands: PO4.17, NDG.19
8 PLIP interactions:8 interactions with chain D- Hydrogen bonds: D:R.79, D:D.124, D:Y.262, D:D.324
- Water bridges: D:R.79, D:K.232, D:D.324
- Salt bridges: D:K.232
BMA.24: 10 residues within 4Å:- Chain D: C.257
- Chain E: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324
- Ligands: PO4.23, NDG.25
8 PLIP interactions:8 interactions with chain E- Hydrogen bonds: E:R.79, E:D.124, E:Y.262, E:D.324
- Water bridges: E:R.79, E:K.232, E:D.324
- Salt bridges: E:K.232
BMA.30: 10 residues within 4Å:- Chain E: C.257
- Chain F: R.79, Y.123, D.124, Y.262, V.301, F.303, D.324
- Ligands: PO4.29, NDG.31
8 PLIP interactions:8 interactions with chain F- Hydrogen bonds: F:R.79, F:D.124, F:Y.262
- Water bridges: F:R.79, F:R.170, F:K.232, F:D.324, F:D.324
- 6 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)
NDG.3: 8 residues within 4Å:- Chain A: R.79, M.87, Y.123, R.170, H.194
- Chain C: F.223, L.254
- Ligands: BMA.2
7 PLIP interactions:5 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:R.79, A:R.79
- Water bridges: A:R.85, A:D.124, C:C.257
- Salt bridges: A:H.194
- Hydrophobic interactions: C:F.223
NDG.9: 9 residues within 4Å:- Chain A: F.223, L.254
- Chain B: R.79, R.85, M.87, Y.123, R.170, H.194
- Ligands: BMA.8
7 PLIP interactions:5 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:R.79, B:R.79
- Water bridges: B:R.85, B:D.324, A:C.257
- Salt bridges: B:H.194
- Hydrophobic interactions: A:F.223
NDG.14: 9 residues within 4Å:- Chain B: F.223, L.254
- Chain C: R.79, M.87, Y.123, R.170, G.193, H.194
- Ligands: BMA.13
7 PLIP interactions:2 interactions with chain B, 5 interactions with chain C- Hydrophobic interactions: B:F.223
- Water bridges: B:C.257, C:R.85, C:D.124
- Hydrogen bonds: C:R.79, C:R.79
- Salt bridges: C:H.194
NDG.19: 9 residues within 4Å:- Chain D: R.79, R.85, M.87, Y.123, R.170, H.194
- Chain F: F.223, L.254
- Ligands: BMA.18
8 PLIP interactions:6 interactions with chain D, 2 interactions with chain F- Hydrogen bonds: D:R.79, D:R.79, D:H.194
- Water bridges: D:R.85, D:Y.123, F:C.257
- Salt bridges: D:H.194
- Hydrophobic interactions: F:F.223
NDG.25: 9 residues within 4Å:- Chain D: F.223, L.254
- Chain E: R.79, R.85, M.87, Y.123, R.170, H.194
- Ligands: BMA.24
8 PLIP interactions:2 interactions with chain D, 6 interactions with chain E- Hydrophobic interactions: D:F.223
- Water bridges: D:C.257, E:R.85, E:Y.123
- Hydrogen bonds: E:R.79, E:R.79, E:H.194
- Salt bridges: E:H.194
NDG.31: 9 residues within 4Å:- Chain E: F.223, L.254
- Chain F: R.79, M.87, Y.123, R.170, H.194
- Ligands: BMA.30, EDO.32
8 PLIP interactions:6 interactions with chain F, 2 interactions with chain E- Hydrogen bonds: F:R.79, F:R.79, F:H.194
- Water bridges: F:R.85, F:Y.123, E:C.257
- Salt bridges: F:H.194
- Hydrophobic interactions: E:F.223
- 3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.4: 5 residues within 4Å:- Chain A: H.143, F.168, N.192
- Chain E: F.197, D.199
1 PLIP interactions:1 interactions with chain A- Water bridges: A:N.192
PGE.20: 5 residues within 4Å:- Chain D: R.133, Y.135, L.161, D.207, M.208
No protein-ligand interaction detected (PLIP)PGE.26: 5 residues within 4Å:- Chain A: F.197
- Chain E: H.143, G.144, F.168, N.192
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain E- Water bridges: A:G.198, A:D.199, E:N.192
- Hydrogen bonds: E:N.192
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 3 residues within 4Å:- Chain A: R.133, Y.135, L.161
No protein-ligand interaction detected (PLIP)EDO.21: 3 residues within 4Å:- Chain D: H.194
- Chain F: H.255, C.257
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:C.257
EDO.28: 4 residues within 4Å:- Chain E: R.133, Y.135, D.207, M.208
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:R.133, E:Y.135
EDO.32: 4 residues within 4Å:- Chain E: F.223
- Chain F: G.193, H.194
- Ligands: NDG.31
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:H.194
- Water bridges: F:Y.121, F:Y.123
EDO.34: 3 residues within 4Å:- Chain F: R.133, Y.135, D.207
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:R.133, F:Y.135
- 6 x K: POTASSIUM ION(Non-covalent)
K.6: 3 residues within 4Å:- Chain A: H.216, V.217, W.275
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:V.217, A:W.275, H2O.5, H2O.6
K.11: 3 residues within 4Å:- Chain B: H.216, V.217, W.275
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:H.216, B:V.217, B:W.275, H2O.14, H2O.15
K.16: 3 residues within 4Å:- Chain C: H.216, V.217, W.275
4 PLIP interactions:2 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:V.217, C:W.275, H2O.23, H2O.24
K.22: 3 residues within 4Å:- Chain D: H.216, V.217, W.275
3 PLIP interactions:1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:W.275, H2O.30, H2O.31
K.27: 3 residues within 4Å:- Chain E: H.216, V.217, W.275
5 PLIP interactions:3 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: E:H.216, E:V.217, E:W.275, H2O.38, H2O.38
K.33: 3 residues within 4Å:- Chain F: H.216, V.217, W.275
4 PLIP interactions:2 interactions with chain F, 2 Ligand-Water interactions- Metal complexes: F:V.217, F:W.275, H2O.44, H2O.45
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.10: 4 residues within 4Å:- Chain B: Y.135, Y.151, D.207, M.208
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.135
GOL.15: 5 residues within 4Å:- Chain C: R.133, Y.135, Y.151, D.207, M.208
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.133
- Water bridges: C:R.133, C:Y.151
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ladeveze, S. et al., Structural Bases for N-Glycan Processing by Mannoside Phosphorylase. Acta Crystallogr.,Sect.D (2015)
- Release Date
- 2015-05-27
- Peptides
- UHGB_MP: ABCDF
UHGB_MP: E - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DF
FE
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.76 Å
- Oligo State
- hetero-5-1-mer
- Ligands
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- 6 x BMA: beta-D-mannopyranose(Non-covalent)
- 6 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)
- 3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 6 x K: POTASSIUM ION(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ladeveze, S. et al., Structural Bases for N-Glycan Processing by Mannoside Phosphorylase. Acta Crystallogr.,Sect.D (2015)
- Release Date
- 2015-05-27
- Peptides
- UHGB_MP: ABCDF
UHGB_MP: E - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DF
FE
E