- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)
- 5 x NO3: NITRATE ION(Non-functional Binders)
NO3.2: 6 residues within 4Å:- Chain A: R.210, T.212, F.310, R.358, Y.362
- Ligands: EDO.5
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:R.210, A:R.210, A:R.358, A:R.358
- Water bridges: A:R.32
NO3.3: 7 residues within 4Å:- Chain A: P.463, Y.468, Y.471, G.472, P.671, Y.672
- Ligands: EDO.9
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.672
NO3.4: 6 residues within 4Å:- Chain A: Y.321, K.322, W.447, K.449, M.450
- Ligands: EDO.8
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:W.447, A:M.450
- Water bridges: A:R.279, A:D.323, A:D.323
NO3.14: 7 residues within 4Å:- Chain B: P.463, Y.468, Y.471, G.472, E.475, P.671, Y.672
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.672
NO3.15: 6 residues within 4Å:- Chain B: Y.321, K.322, W.447, K.449, M.450
- Ligands: EDO.17
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Y.321, B:M.450
- Water bridges: B:R.279, B:K.449
- 9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 7 residues within 4Å:- Chain A: V.162, Y.165, N.166, Y.362, F.364
- Ligands: NDG.1, NO3.2
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.166, A:N.166
- Water bridges: A:Y.165
EDO.6: 7 residues within 4Å:- Chain A: W.315, I.316, G.317, T.318, E.319, P.320, R.451
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:G.317, A:T.318, A:T.318, A:E.319, A:E.319
- Water bridges: A:R.451
EDO.7: 6 residues within 4Å:- Chain A: Y.75, K.111, Y.112, L.245, R.255, L.256
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:K.111, A:R.255, A:L.256
- Water bridges: A:L.245, A:L.256
EDO.8: 7 residues within 4Å:- Chain A: W.447, G.448, K.449, F.486, S.488, D.491
- Ligands: NO3.4
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.449, A:S.488, A:S.488
- Water bridges: A:K.449
EDO.9: 6 residues within 4Å:- Chain A: D.339, K.384, Y.471, E.475, Y.672
- Ligands: NO3.3
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.339, A:K.384
- Water bridges: A:K.384
EDO.16: 7 residues within 4Å:- Chain B: W.315, I.316, G.317, T.318, E.319, P.320, R.451
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:G.317, B:T.318, B:T.318, B:E.319, B:E.319
- Water bridges: B:F.234, B:R.451
EDO.17: 8 residues within 4Å:- Chain B: W.447, G.448, K.449, F.486, I.487, S.488, D.491
- Ligands: NO3.15
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:K.449, B:S.488, B:S.488
- Water bridges: B:K.449, B:K.449, B:K.449
EDO.18: 4 residues within 4Å:- Chain B: L.379, H.418, D.743, S.744
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:H.418, B:D.743
EDO.19: 5 residues within 4Å:- Chain B: V.116, R.118, G.121, R.257, E.259
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.257, B:R.257
- 8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.10: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.11: 1 residues within 4Å:- Chain A: R.272
No protein-ligand interaction detected (PLIP)MG.12: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.20: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.21: 1 residues within 4Å:- Chain B: D.595
4 PLIP interactions:1 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:D.595, H2O.67, H2O.67, H2O.68
MG.22: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.23: 1 residues within 4Å:- Chain B: D.247
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.247, H2O.49, H2O.68
MG.24: 1 residues within 4Å:- Chain B: R.272
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hidaka, M. et al., The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold. J.Biol.Chem. (2009)
- Release Date
- 2008-12-30
- Peptides
- Lacto-N-biose phosphorylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.85 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)
- 5 x NO3: NITRATE ION(Non-functional Binders)
- 9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hidaka, M. et al., The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold. J.Biol.Chem. (2009)
- Release Date
- 2008-12-30
- Peptides
- Lacto-N-biose phosphorylase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B