- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BGC- GAL- NAG- NAG: 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 UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
UDP.4: 13 residues within 4Å:- Chain A: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, W.199, H.232, D.235
- Ligands: MN.5, GOL.13
19 PLIP interactions:19 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
- Water bridges: A:R.74, A:R.74, A:K.164, A:N.238, A:N.238, A:N.238
- Salt bridges: A:R.76, A:H.232, A:H.232
- pi-Stacking: A:F.111
- pi-Cation interactions: A:R.76
UDP.14: 17 residues within 4Å:- Chain B: P.72, F.73, R.74, R.76, F.111, R.113, D.137, V.138, D.139, W.199, H.229, H.232, D.235, N.238
- Ligands: MN.15, SO4.21, GOL.27
18 PLIP interactions:18 interactions with chain B- Hydrogen bonds: B:P.72, B:R.74, B:R.74, B:R.76, B:V.138, B:D.139
- Water bridges: B:R.74, B:D.137, B:D.137, B:D.235, B:D.235, B:N.238
- Salt bridges: B:R.76, B:K.164, B:H.232, B:H.232
- pi-Stacking: B:F.111
- pi-Cation interactions: B:R.76
UDP.29: 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.30, GOL.35
18 PLIP interactions:18 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.235, C:D.235, C:N.238
- Water bridges: C:D.137, C:D.137, C:K.164
- 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.39: 13 residues within 4Å:- Chain D: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, W.199, H.232, D.235
- Ligands: MN.40, GOL.48
20 PLIP interactions:20 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
- Water bridges: D:R.74, D:R.74, D:D.137, D:D.137, D:K.164, D:N.238, D:N.238, D:N.238
- Salt bridges: D:R.76, D:H.232, D:H.232
- pi-Stacking: D:F.111
- pi-Cation interactions: D:R.76
UDP.49: 17 residues within 4Å:- Chain E: P.72, F.73, R.74, R.76, F.111, R.113, D.137, V.138, D.139, W.199, H.229, H.232, D.235, N.238
- Ligands: MN.50, SO4.56, GOL.62
17 PLIP interactions:17 interactions with chain E- Hydrogen bonds: E:P.72, E:R.74, E:R.74, E:R.76, E:V.138, E:D.139
- Water bridges: E:R.74, E:D.235, E:N.238, E:N.238, E:N.238
- Salt bridges: E:R.76, E:K.164, E:H.232, E:H.232
- pi-Stacking: E:F.111
- pi-Cation interactions: E:R.76
UDP.64: 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.65, GOL.70
15 PLIP interactions:15 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.235, F:N.238
- Water bridges: F:K.164
- 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
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.139, A:H.229, A:H.232
MN.15: 4 residues within 4Å:- Chain B: D.139, H.229, H.232
- Ligands: UDP.14
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.139, B:H.229, B:H.232
MN.30: 4 residues within 4Å:- Chain C: D.139, H.229, H.232
- Ligands: UDP.29
3 PLIP interactions:3 interactions with chain C- Metal complexes: C:D.139, C:H.229, C:H.232
MN.40: 4 residues within 4Å:- Chain D: D.139, H.229, H.232
- Ligands: UDP.39
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.139, D:H.229, D:H.232
MN.50: 4 residues within 4Å:- Chain E: D.139, H.229, H.232
- Ligands: UDP.49
3 PLIP interactions:3 interactions with chain E- Metal complexes: E:D.139, E:H.229, E:H.232
MN.65: 4 residues within 4Å:- Chain F: D.139, H.229, H.232
- Ligands: UDP.64
3 PLIP interactions:3 interactions with chain F- Metal complexes: F:D.139, F:H.229, F:H.232
- 44 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: 2 residues within 4Å:- Chain A: R.156, P.220
Ligand excluded by PLIPSO4.9: 2 residues within 4Å:- Chain A: T.264, Y.265
Ligand excluded by PLIPSO4.10: 8 residues within 4Å:- Chain A: F.207, M.215, S.216, I.217
- Chain E: F.207, V.211, S.216, I.217
Ligand excluded by PLIPSO4.11: 2 residues within 4Å:- Chain A: N.195, R.247
Ligand excluded by PLIPSO4.12: 7 residues within 4Å:- Chain A: P.37, V.38, D.39, L.42, V.43, Q.46, Y.85
Ligand excluded by PLIPSO4.16: 3 residues within 4Å:- Chain B: H.79, H.232, S.233
Ligand excluded by PLIPSO4.17: 5 residues within 4Å:- Chain B: E.33, F.34, N.35, R.228, R.231
Ligand excluded by PLIPSO4.18: 5 residues within 4Å:- Chain B: N.195, W.197, R.247, P.286, S.287
Ligand excluded by PLIPSO4.19: 5 residues within 4Å:- Chain B: Y.171, D.204, F.245
- Ligands: BGC-GAL-NAG-NAG.2, BGC-GAL-NAG-NAG.2
Ligand excluded by PLIPSO4.20: 3 residues within 4Å:- Chain B: F.152, R.156, P.220
Ligand excluded by PLIPSO4.21: 2 residues within 4Å:- Chain B: W.199
- Ligands: UDP.14
Ligand excluded by PLIPSO4.22: 4 residues within 4Å:- Chain B: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.23: 5 residues within 4Å:- Chain B: M.36, P.37, V.38, D.39, Y.85
Ligand excluded by PLIPSO4.24: 2 residues within 4Å:- Chain B: K.51, M.52
Ligand excluded by PLIPSO4.25: 2 residues within 4Å:- Chain B: G.284, T.285
Ligand excluded by PLIPSO4.26: 5 residues within 4Å:- Chain B: L.125, K.126, D.127, Y.128, D.129
Ligand excluded by PLIPSO4.31: 4 residues within 4Å:- Chain C: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.32: 4 residues within 4Å:- Chain C: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.33: 3 residues within 4Å:- Chain C: F.152, R.156, P.220
Ligand excluded by PLIPSO4.34: 2 residues within 4Å:- Chain C: H.232, S.233
Ligand excluded by PLIPSO4.41: 4 residues within 4Å:- Chain D: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.42: 5 residues within 4Å:- Chain D: N.49, Y.56, P.58, R.59, D.60
Ligand excluded by PLIPSO4.43: 2 residues within 4Å:- Chain D: R.156, P.220
Ligand excluded by PLIPSO4.44: 2 residues within 4Å:- Chain D: T.264, Y.265
Ligand excluded by PLIPSO4.45: 8 residues within 4Å:- Chain B: F.207, V.211, S.216, I.217
- Chain D: F.207, M.215, S.216, I.217
Ligand excluded by PLIPSO4.46: 2 residues within 4Å:- Chain D: N.195, R.247
Ligand excluded by PLIPSO4.47: 7 residues within 4Å:- Chain D: P.37, V.38, D.39, L.42, V.43, Q.46, Y.85
Ligand excluded by PLIPSO4.51: 3 residues within 4Å:- Chain E: H.79, H.232, S.233
Ligand excluded by PLIPSO4.52: 5 residues within 4Å:- Chain E: E.33, F.34, N.35, R.228, R.231
Ligand excluded by PLIPSO4.53: 5 residues within 4Å:- Chain E: N.195, W.197, R.247, P.286, S.287
Ligand excluded by PLIPSO4.54: 5 residues within 4Å:- Chain E: Y.171, D.204, F.245
- Ligands: BGC-GAL-NAG-NAG.37, BGC-GAL-NAG-NAG.37
Ligand excluded by PLIPSO4.55: 3 residues within 4Å:- Chain E: F.152, R.156, P.220
Ligand excluded by PLIPSO4.56: 2 residues within 4Å:- Chain E: W.199
- Ligands: UDP.49
Ligand excluded by PLIPSO4.57: 4 residues within 4Å:- Chain E: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.58: 5 residues within 4Å:- Chain E: M.36, P.37, V.38, D.39, Y.85
Ligand excluded by PLIPSO4.59: 2 residues within 4Å:- Chain E: K.51, M.52
Ligand excluded by PLIPSO4.60: 2 residues within 4Å:- Chain E: G.284, T.285
Ligand excluded by PLIPSO4.61: 5 residues within 4Å:- Chain E: L.125, K.126, D.127, Y.128, D.129
Ligand excluded by PLIPSO4.66: 4 residues within 4Å:- Chain F: N.49, Y.56, P.58, R.59
Ligand excluded by PLIPSO4.67: 4 residues within 4Å:- Chain F: E.33, F.34, N.35, R.228
Ligand excluded by PLIPSO4.68: 3 residues within 4Å:- Chain F: F.152, R.156, P.220
Ligand excluded by PLIPSO4.69: 2 residues within 4Å:- Chain F: H.232, S.233
Ligand excluded by PLIP- 8 x GOL: GLYCEROL(Non-functional Binders)
GOL.13: 7 residues within 4Å:- Chain A: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-NAG.1, UDP.4
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.137, A:G.200, A:D.203
GOL.27: 7 residues within 4Å:- Chain B: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-NAG.2, UDP.14
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.200, B:E.202
- Water bridges: B:G.198, B:E.202, B:N.238
GOL.28: 4 residues within 4Å:- Chain B: F.73, R.74, N.75, N.104
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:N.75, B:N.75, B:N.75, B:N.104
GOL.35: 7 residues within 4Å:- Chain C: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-NAG.3, UDP.29
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:W.199, C:G.200, C:D.203
GOL.48: 7 residues within 4Å:- Chain D: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-NAG.36, UDP.39
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:D.137, D:G.200, D:D.203
GOL.62: 7 residues within 4Å:- Chain E: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-NAG.37, UDP.49
6 PLIP interactions:6 interactions with chain E- Hydrogen bonds: E:R.113, E:G.200, E:E.202
- Water bridges: E:G.198, E:E.202, E:N.238
GOL.63: 4 residues within 4Å:- Chain E: F.73, R.74, N.75, N.104
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:N.75, E:N.75, E:N.75, E:N.104
GOL.70: 7 residues within 4Å:- Chain F: R.113, W.199, G.200, E.202, D.203
- Ligands: BGC-GAL-NAG-NAG.38, UDP.64
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:W.199, F:G.200, F:D.203
- 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 1.95 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BGC- GAL- NAG- NAG: 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 UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)
- 6 x MN: MANGANESE (II) ION(Non-covalent)
- 44 x SO4: SULFATE ION(Non-functional Binders)
- 8 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