- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BGC- GAL- NAG- GAL- NAG: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
- 6 x UDH: 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE(Non-covalent)
UDH.4: 16 residues within 4Å:- Chain A: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, H.232, D.235, N.238
- Ligands: MN.5, GOL.14
21 PLIP interactions:21 interactions with chain A- Hydrophobic interactions: A:D.235
- Hydrogen bonds: A:P.72, A:R.74, A:R.74, A:R.76, A:V.138, A:D.139, A:D.235, A:D.235
- Water bridges: A:R.74, A:K.164, A:K.164, A:N.238, A:N.238
- Salt bridges: A:R.76, A:K.164, A:H.229, A:H.232, A:H.232
- pi-Stacking: A:F.111
- pi-Cation interactions: A:R.76
UDH.15: 16 residues within 4Å:- Chain B: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, H.232, D.235, N.238
- Ligands: MN.16, GOL.23
20 PLIP interactions:20 interactions with chain B- Hydrogen bonds: B:P.72, B:R.74, B:R.74, B:R.76, B:V.138, B:D.139, B:D.235, B:D.235, B:N.238
- Water bridges: B:R.74, B:K.164, B:K.164, B:K.164
- Salt bridges: B:R.76, B:K.164, B:H.229, B:H.232, B:H.232
- pi-Stacking: B:F.111
- pi-Cation interactions: B:R.76
UDH.24: 17 residues within 4Å:- Chain C: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, R.231, H.232, R.234, D.235
- Ligands: MN.25, GOL.30
22 PLIP interactions:22 interactions with chain C- Hydrophobic interactions: C:R.234
- Hydrogen bonds: C:P.72, C:R.74, C:R.74, C:R.76, C:V.138, C:D.139, C:R.231, C:R.234, C:D.235, C:D.235
- Water bridges: C:R.74, C:D.137, C:N.238, C:N.238
- Salt bridges: C:R.76, C:K.164, C:H.229, C:H.232, C:H.232
- pi-Stacking: C:F.111
- pi-Cation interactions: C:R.76
UDH.34: 16 residues within 4Å:- Chain D: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, H.232, D.235, N.238
- Ligands: MN.35, GOL.44
22 PLIP interactions:22 interactions with chain D- Hydrophobic interactions: D:D.235
- Hydrogen bonds: D:P.72, D:R.74, D:R.74, D:R.76, D:V.138, D:D.139, D:D.235
- Water bridges: D:R.74, D:D.137, D:D.137, D:D.137, D:K.164, D:N.238, D:N.238
- Salt bridges: D:R.76, D:K.164, D:H.229, D:H.232, D:H.232
- pi-Stacking: D:F.111
- pi-Cation interactions: D:R.76
UDH.45: 16 residues within 4Å:- Chain E: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, H.232, D.235, N.238
- Ligands: MN.46, GOL.53
19 PLIP interactions:19 interactions with chain E- Hydrogen bonds: E:P.72, E:R.74, E:R.74, E:R.76, E:V.138, E:D.139, E:D.235, E:N.238
- Water bridges: E:R.74, E:D.137, E:D.137, E:K.164
- Salt bridges: E:R.76, E:K.164, E:H.229, E:H.232, E:H.232
- pi-Stacking: E:F.111
- pi-Cation interactions: E:R.76
UDH.54: 17 residues within 4Å:- Chain F: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, R.231, H.232, R.234, D.235
- Ligands: MN.55, GOL.60
20 PLIP interactions:20 interactions with chain F- Hydrophobic interactions: F:R.234
- Hydrogen bonds: F:P.72, F:R.74, F:R.74, F:R.76, F:V.138, F:D.139, F:R.231, F:R.234, F:D.235
- Water bridges: F:R.74, F:N.238, F:N.238
- Salt bridges: F:R.76, F:K.164, F:H.229, F:H.232, F:H.232
- pi-Stacking: F:F.111
- pi-Cation interactions: F:R.76
- 6 x MN: MANGANESE (II) ION(Non-covalent)
MN.5: 4 residues within 4Å:- Chain A: D.139, H.229, H.232
- Ligands: UDH.4
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.139, A:H.229, A:H.232, H2O.1
MN.16: 4 residues within 4Å:- Chain B: D.139, H.229, H.232
- Ligands: UDH.15
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.139, B:H.229, B:H.232, H2O.10
MN.25: 4 residues within 4Å:- Chain C: D.139, H.229, H.232
- Ligands: UDH.24
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.139, C:H.229, C:H.232, H2O.16
MN.35: 4 residues within 4Å:- Chain D: D.139, H.229, H.232
- Ligands: UDH.34
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.139, D:H.229, D:H.232, H2O.22
MN.46: 4 residues within 4Å:- Chain E: D.139, H.229, H.232
- Ligands: UDH.45
4 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.139, E:H.229, E:H.232, H2O.30
MN.55: 4 residues within 4Å:- Chain F: D.139, H.229, H.232
- Ligands: UDH.54
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:D.139, F:H.229, F:H.232, H2O.36
- 36 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 4 residues within 4Å:- Chain A: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.7: 5 residues within 4Å:- Chain A: N.49, Y.56, P.58, R.59, D.60
Ligand excluded by PLIPSO4.8: 4 residues within 4Å:- Chain A: Q.122, L.263, T.264, Y.265
Ligand excluded by PLIPSO4.9: 4 residues within 4Å:- Chain A: F.152, R.156, R.219, P.220
Ligand excluded by PLIPSO4.10: 2 residues within 4Å:- Chain A: S.257, D.258
Ligand excluded by PLIPSO4.11: 2 residues within 4Å:- Chain A: F.152, S.153
Ligand excluded by PLIPSO4.12: 2 residues within 4Å:- Chain A: H.232, S.233
Ligand excluded by PLIPSO4.13: 6 residues within 4Å:- Chain A: F.207, S.216, I.217
- Chain E: F.207, S.216, I.217
Ligand excluded by PLIPSO4.17: 4 residues within 4Å:- Chain B: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.18: 7 residues within 4Å:- Chain B: E.33, F.34, N.35, R.228, R.231
- Chain C: P.48, N.49
Ligand excluded by PLIPSO4.19: 5 residues within 4Å:- Chain B: N.195, W.197, R.247, P.286, S.287
Ligand excluded by PLIPSO4.20: 2 residues within 4Å:- Chain B: H.232, S.233
Ligand excluded by PLIPSO4.21: 3 residues within 4Å:- Chain B: F.152, R.156, P.220
Ligand excluded by PLIPSO4.22: 5 residues within 4Å:- Chain B: V.38, D.39, L.40, E.41, K.81
Ligand excluded by PLIPSO4.26: 4 residues within 4Å:- Chain C: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.27: 2 residues within 4Å:- Chain C: F.152, S.153
Ligand excluded by PLIPSO4.28: 4 residues within 4Å:- Chain C: N.195, W.197, P.286, S.287
Ligand excluded by PLIPSO4.29: 6 residues within 4Å:- Chain A: P.48, N.49
- Chain C: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.36: 4 residues within 4Å:- Chain D: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.37: 5 residues within 4Å:- Chain D: N.49, Y.56, P.58, R.59, D.60
Ligand excluded by PLIPSO4.38: 4 residues within 4Å:- Chain D: Q.122, L.263, T.264, Y.265
Ligand excluded by PLIPSO4.39: 4 residues within 4Å:- Chain D: F.152, R.156, R.219, P.220
Ligand excluded by PLIPSO4.40: 2 residues within 4Å:- Chain D: S.257, D.258
Ligand excluded by PLIPSO4.41: 2 residues within 4Å:- Chain D: F.152, S.153
Ligand excluded by PLIPSO4.42: 2 residues within 4Å:- Chain D: H.232, S.233
Ligand excluded by PLIPSO4.43: 6 residues within 4Å:- Chain B: F.207, S.216, I.217
- Chain D: F.207, S.216, I.217
Ligand excluded by PLIPSO4.47: 4 residues within 4Å:- Chain E: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.48: 7 residues within 4Å:- Chain E: E.33, F.34, N.35, R.228, R.231
- Chain F: P.48, N.49
Ligand excluded by PLIPSO4.49: 5 residues within 4Å:- Chain E: N.195, W.197, R.247, P.286, S.287
Ligand excluded by PLIPSO4.50: 2 residues within 4Å:- Chain E: H.232, S.233
Ligand excluded by PLIPSO4.51: 3 residues within 4Å:- Chain E: F.152, R.156, P.220
Ligand excluded by PLIPSO4.52: 5 residues within 4Å:- Chain E: V.38, D.39, L.40, E.41, K.81
Ligand excluded by PLIPSO4.56: 4 residues within 4Å:- Chain F: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.57: 2 residues within 4Å:- Chain F: F.152, S.153
Ligand excluded by PLIPSO4.58: 4 residues within 4Å:- Chain F: N.195, W.197, P.286, S.287
Ligand excluded by PLIPSO4.59: 6 residues within 4Å:- Chain D: P.48, N.49
- Chain F: E.33, F.34, N.35, R.228
Ligand excluded by PLIP- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.14: 9 residues within 4Å:- Chain A: R.113, D.137, G.177, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-GAL-NAG.1, UDH.4
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:R.113, A:G.177, A:W.199, A:G.200
- Water bridges: A:G.198, A:G.200
GOL.23: 7 residues within 4Å:- Chain B: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-GAL-NAG.2, UDH.15
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:R.113, B:W.199, B:G.200
- Water bridges: B:G.198, B:E.202
GOL.30: 9 residues within 4Å:- Chain C: R.113, D.137, G.176, G.177, W.199, G.200, E.202
- Ligands: BGC-GAL-NAG-GAL-NAG.3, UDH.24
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:R.113, C:G.177, C:W.199, C:G.200
- Water bridges: C:Y.174
GOL.44: 9 residues within 4Å:- Chain D: R.113, D.137, G.177, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-GAL-NAG.31, UDH.34
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:R.113, D:G.177, D:W.199, D:G.200
- Water bridges: D:G.198, D:G.200
GOL.53: 7 residues within 4Å:- Chain E: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-GAL-NAG.32, UDH.45
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:R.113, E:W.199, E:G.200
- Water bridges: E:G.198, E:E.202
GOL.60: 9 residues within 4Å:- Chain F: R.113, D.137, G.176, G.177, W.199, G.200, E.202
- Ligands: BGC-GAL-NAG-GAL-NAG.33, UDH.54
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:R.113, F:G.177, F:W.199, F:G.200
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ramakrishnan, B. et al., Binding of N-acetylglucosamine (GlcNAc) beta 1-6-branched oligosaccharide acceptors to beta 4-galactosyltransferase I reveals a new ligand binding mode. J.Biol.Chem. (2012)
- Release Date
- 2012-07-04
- Peptides
- Beta-1,4-galactosyltransferase 1: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
AE
BF
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BGC- GAL- NAG- GAL- NAG: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
- 6 x UDH: 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)
- 36 x SO4: SULFATE ION(Non-functional Binders)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Ramakrishnan, B. et al., Binding of N-acetylglucosamine (GlcNAc) beta 1-6-branched oligosaccharide acceptors to beta 4-galactosyltransferase I reveals a new ligand binding mode. J.Biol.Chem. (2012)
- Release Date
- 2012-07-04
- Peptides
- Beta-1,4-galactosyltransferase 1: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
AE
BF
C