- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BGC- GAL- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
- 6 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
UDP.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.6
20 PLIP interactions:20 interactions with chain A- 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
UDP.11: 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.12, GOL.13
22 PLIP interactions:22 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
- Water bridges: B:R.74, B:K.164, B:K.164, B:K.164, B:K.164, B:N.238, B:N.238
- 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
UDP.20: 16 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, H.232, D.235, N.238
- Ligands: MN.21, GOL.22
19 PLIP interactions:19 interactions with chain C- Hydrogen bonds: C:P.72, C:R.74, C:R.74, C:R.76, C:V.138, C:D.139, C:D.139, C:W.199, C:D.235, C:D.235
- Water bridges: C:D.137, C:K.164, C:K.236
- Salt bridges: C:R.76, C:K.164, C:H.232, C:H.232
- pi-Stacking: C:F.111
- pi-Cation interactions: C:R.76
UDP.28: 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.29, GOL.30
21 PLIP interactions:21 interactions with chain D- 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:K.164, 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
UDP.35: 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.36, GOL.37
21 PLIP interactions:21 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
- Water bridges: E:R.74, E:D.137, E:D.137, E:K.164, E:K.164, E:N.238, E:N.238
- 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
UDP.44: 16 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, H.232, D.235, N.238
- Ligands: MN.45, GOL.46
18 PLIP interactions:18 interactions with chain F- Hydrogen bonds: F:P.72, F:R.74, F:R.74, F:R.76, F:V.138, F:D.139, F:D.139, F:W.199, F:D.235
- Water bridges: F:K.164, F:K.164, F:K.236
- Salt bridges: F:R.76, F:K.164, 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: UDP.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.2
MN.12: 4 residues within 4Å:- Chain B: D.139, H.229, H.232
- Ligands: UDP.11
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.139, B:H.229, B:H.232
MN.21: 5 residues within 4Å:- Chain C: D.139, K.164, H.229, H.232
- Ligands: UDP.20
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.139, C:H.229, C:H.232, H2O.18
MN.29: 4 residues within 4Å:- Chain D: D.139, H.229, H.232
- Ligands: UDP.28
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.36: 4 residues within 4Å:- Chain E: D.139, H.229, H.232
- Ligands: UDP.35
3 PLIP interactions:3 interactions with chain E- Metal complexes: E:D.139, E:H.229, E:H.232
MN.45: 5 residues within 4Å:- Chain F: D.139, K.164, H.229, H.232
- Ligands: UDP.44
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:D.139, F:H.229, F:H.232, H2O.37
- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.6: 8 residues within 4Å:- Chain A: R.113, D.137, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG.1, UDP.4
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.137, A:G.200, A:E.202, A:D.203
- Water bridges: A:N.238
GOL.13: 7 residues within 4Å:- Chain B: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG.2, UDP.11
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.200, B:E.202
- Water bridges: B:G.198, B:G.200, B:N.238
GOL.14: 4 residues within 4Å:- Chain B: F.73, R.74, N.75, N.104
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.75, B:N.75, B:N.104
GOL.22: 7 residues within 4Å:- Chain C: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG.3, UDP.20
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:G.200, C:D.203
- Water bridges: C:G.177, C:G.177, C:G.198, C:G.200
GOL.30: 8 residues within 4Å:- Chain D: R.113, D.137, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG.25, UDP.28
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:D.137, D:G.200, D:E.202, D:D.203
- Water bridges: D:N.238
GOL.37: 7 residues within 4Å:- Chain E: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG.26, UDP.35
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:G.200, E:E.202
- Water bridges: E:G.198, E:E.202, E:N.238
GOL.38: 4 residues within 4Å:- Chain E: F.73, R.74, N.75, N.104
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:N.75, E:N.75, E:N.104
GOL.46: 7 residues within 4Å:- Chain F: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG.27, UDP.44
6 PLIP interactions:6 interactions with chain F- Hydrogen bonds: F:G.200, F:D.203
- Water bridges: F:G.177, F:G.177, F:G.198, F:G.200
- 22 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 4 residues within 4Å:- Chain A: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.8: 5 residues within 4Å:- Chain A: N.49, Y.56, P.58, R.59, D.60
Ligand excluded by PLIPSO4.9: 3 residues within 4Å:- Chain A: F.152, R.156, P.220
Ligand excluded by PLIPSO4.10: 3 residues within 4Å:- Chain A: L.263, T.264, Y.265
Ligand excluded by PLIPSO4.15: 6 residues within 4Å:- Chain B: E.33, F.34, N.35, R.228, R.231
- Chain C: N.49
Ligand excluded by PLIPSO4.16: 3 residues within 4Å:- Chain B: R.231, H.232, S.233
Ligand excluded by PLIPSO4.17: 2 residues within 4Å:- Chain B: R.156, P.220
Ligand excluded by PLIPSO4.18: 4 residues within 4Å:- Chain B: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.19: 5 residues within 4Å:- Chain B: V.38, D.39, L.40, E.41, K.81
Ligand excluded by PLIPSO4.23: 3 residues within 4Å:- Chain C: F.34, N.35, R.228
Ligand excluded by PLIPSO4.24: 4 residues within 4Å:- Chain C: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.31: 4 residues within 4Å:- Chain D: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.32: 5 residues within 4Å:- Chain D: N.49, Y.56, P.58, R.59, D.60
Ligand excluded by PLIPSO4.33: 3 residues within 4Å:- Chain D: F.152, R.156, P.220
Ligand excluded by PLIPSO4.34: 3 residues within 4Å:- Chain D: L.263, T.264, Y.265
Ligand excluded by PLIPSO4.39: 6 residues within 4Å:- Chain E: E.33, F.34, N.35, R.228, R.231
- Chain F: N.49
Ligand excluded by PLIPSO4.40: 3 residues within 4Å:- Chain E: R.231, H.232, S.233
Ligand excluded by PLIPSO4.41: 2 residues within 4Å:- Chain E: R.156, P.220
Ligand excluded by PLIPSO4.42: 4 residues within 4Å:- Chain E: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.43: 5 residues within 4Å:- Chain E: V.38, D.39, L.40, E.41, K.81
Ligand excluded by PLIPSO4.47: 3 residues within 4Å:- Chain F: F.34, N.35, R.228
Ligand excluded by PLIPSO4.48: 4 residues within 4Å:- Chain F: N.49, Y.56, P.58, R.59
Ligand excluded by PLIP- 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 2.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BGC- GAL- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
- 6 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)
- 8 x GOL: GLYCEROL(Non-functional Binders)
- 22 x SO4: SULFATE ION(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