SMTL ID : 7bb4.1

Crystal structure of perdeuterated PLL lectin in complex with L-fucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

16 x FUL: beta-L-fucopyranose(Non-covalent)

FUL.1: 10 residues within 4Å: Chain A: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUC.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.121, A:W.147 Hydrogen bonds: A:G.120, A:G.120, A:S.142, A:S.142 Water bridges: A:G.119, A:G.119 FUL.3: 10 residues within 4Å: Chain A: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.114 Hydrogen bonds: A:V.72, A:T.94, A:D.95 Water bridges: A:D.95 FUL.13: 7 residues within 4Å: Chain A: I.311, I.312, G.332, L.333, D.334, W.338, W.354 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.354 Hydrogen bonds: A:L.333, A:D.334, A:D.334 Water bridges: A:I.311 FUL.16: 8 residues within 4Å: Chain A: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.195 Hydrogen bonds: A:T.168, A:T.168, A:A.190, A:D.191 FUL.17: 10 residues within 4Å: Chain B: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUC.18 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.121, B:W.147 Hydrogen bonds: B:G.120, B:G.120, B:S.142, B:S.142 Water bridges: B:G.119, B:G.119 FUL.19: 10 residues within 4Å: Chain B: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.20 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.114 Hydrogen bonds: B:V.72, B:T.94, B:D.95 Water bridges: B:D.95 FUL.29: 7 residues within 4Å: Chain B: I.311, I.312, G.332, L.333, D.334, W.338, W.354 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.354 Hydrogen bonds: B:L.333, B:D.334, B:D.334 Water bridges: B:I.311 FUL.32: 8 residues within 4Å: Chain B: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.31 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.195 Hydrogen bonds: B:T.168, B:T.168, B:A.190, B:D.191 FUL.33: 10 residues within 4Å: Chain C: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUC.34 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.121, C:W.147 Hydrogen bonds: C:G.120, C:G.120, C:S.142, C:S.142 Water bridges: C:G.119, C:G.119 FUL.35: 10 residues within 4Å: Chain C: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.36 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.114 Hydrogen bonds: C:V.72, C:T.94, C:D.95 FUL.45: 7 residues within 4Å: Chain C: I.311, I.312, G.332, L.333, D.334, W.338, W.354 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.354 Hydrogen bonds: C:L.333, C:D.334, C:D.334 Water bridges: C:I.311 FUL.48: 8 residues within 4Å: Chain C: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.47 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.195 Hydrogen bonds: C:T.168, C:T.168, C:T.168, C:A.190, C:D.191 FUL.49: 10 residues within 4Å: Chain D: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUC.50 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.121, D:W.147 Hydrogen bonds: D:G.120, D:G.120, D:S.142, D:S.142 Water bridges: D:G.119, D:G.119 FUL.51: 10 residues within 4Å: Chain D: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUC.52 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.114 Hydrogen bonds: D:V.72, D:T.94, D:D.95 FUL.61: 7 residues within 4Å: Chain D: I.311, I.312, G.332, L.333, D.334, W.338, W.354 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.354 Hydrogen bonds: D:L.333, D:D.334, D:D.334 Water bridges: D:I.311 FUL.64: 8 residues within 4Å: Chain D: G.167, T.168, G.189, A.190, D.191, W.195, W.210 Ligands: FUC.63 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.195 Hydrogen bonds: D:T.168, D:T.168, D:T.168, D:A.190, D:D.191

12 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.2: 10 residues within 4Å: Chain A: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.121, A:W.147 Hydrogen bonds: A:G.120, A:G.120, A:S.142, A:S.142 Water bridges: A:G.119 FUC.4: 10 residues within 4Å: Chain A: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.73, A:W.114 Hydrogen bonds: A:T.94 Water bridges: A:V.72, A:D.95, A:D.95 FUC.15: 7 residues within 4Å: Chain A: G.167, T.168, G.189, A.190, W.195, W.210 Ligands: FUL.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.210 Hydrogen bonds: A:T.168, A:A.190, A:D.191 FUC.18: 10 residues within 4Å: Chain B: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.17 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.121, B:W.147 Hydrogen bonds: B:G.120, B:G.120, B:S.142, B:S.142 Water bridges: B:G.119 FUC.20: 10 residues within 4Å: Chain B: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.19 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.73, B:W.114 Hydrogen bonds: B:T.94 Water bridges: B:V.72, B:D.95, B:D.95 FUC.31: 7 residues within 4Å: Chain B: G.167, T.168, G.189, A.190, W.195, W.210 Ligands: FUL.32 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.210 Hydrogen bonds: B:T.168, B:A.190, B:D.191 FUC.34: 10 residues within 4Å: Chain C: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.33 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.121, C:W.147 Hydrogen bonds: C:G.120, C:G.120, C:S.142, C:D.143 Water bridges: C:G.119 FUC.36: 10 residues within 4Å: Chain C: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.35 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.73, C:W.114 Hydrogen bonds: C:T.94 Water bridges: C:V.72, C:D.95 FUC.47: 7 residues within 4Å: Chain C: G.167, T.168, G.189, A.190, W.195, W.210 Ligands: FUL.48 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.210 Hydrogen bonds: C:T.168, C:A.190, C:D.191 Water bridges: C:T.168 FUC.50: 10 residues within 4Å: Chain D: G.119, G.120, I.121, V.139, G.141, S.142, D.143, W.147, W.162 Ligands: FUL.49 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.121, D:W.147 Hydrogen bonds: D:G.120, D:G.120, D:S.142, D:S.142 Water bridges: D:G.119 FUC.52: 10 residues within 4Å: Chain D: G.71, V.72, V.73, V.91, G.93, T.94, D.95, W.99, W.114 Ligands: FUL.51 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.73, D:W.114 Hydrogen bonds: D:T.94 Water bridges: D:V.72, D:D.95 FUC.63: 7 residues within 4Å: Chain D: G.167, T.168, G.189, A.190, W.195, W.210 Ligands: FUL.64 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.210 Hydrogen bonds: D:T.168, D:A.190, D:D.191 Water bridges: D:T.168

36 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 11 residues within 4Å: Chain A: Q.54, L.58, P.59, N.60, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.6: 11 residues within 4Å: Chain A: N.33, R.37, E.39, H.51, W.53, Q.103, D.107, T.108, N.109, W.111 Ligands: GOL.10 Ligand excluded by PLIP GOL.7: 10 residues within 4Å: Chain A: N.130, R.134, E.136, H.148, W.150, Q.199, H.203, T.204, D.205, W.207 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: N.178, R.182, E.184, H.196, W.198, Q.247, V.253, W.255 Ligand excluded by PLIP GOL.9: 10 residues within 4Å: Chain A: N.82, R.86, E.88, H.100, W.102, Q.151, H.155, T.156, N.157, W.159 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: D.35, R.37, T.55, D.107 Ligands: GOL.6 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: T.74, S.75, R.92, A.365, S.366, V.367, I.368 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: D.262, G.263, N.304, W.305 Chain C: N.257 Ligand excluded by PLIP GOL.21: 11 residues within 4Å: Chain B: Q.54, L.58, P.59, N.60, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.22: 11 residues within 4Å: Chain B: N.33, R.37, E.39, H.51, W.53, Q.103, D.107, T.108, N.109, W.111 Ligands: GOL.26 Ligand excluded by PLIP GOL.23: 10 residues within 4Å: Chain B: N.130, R.134, E.136, H.148, W.150, Q.199, H.203, T.204, D.205, W.207 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain B: N.178, R.182, E.184, H.196, W.198, Q.247, V.253, W.255 Ligand excluded by PLIP GOL.25: 10 residues within 4Å: Chain B: N.82, R.86, E.88, H.100, W.102, Q.151, H.155, T.156, N.157, W.159 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: D.35, R.37, T.55, D.107 Ligands: GOL.22 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain B: T.74, S.75, R.92, A.365, S.366, V.367, I.368 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain B: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain B: D.262, G.263, N.304, W.305 Chain D: N.257 Ligand excluded by PLIP GOL.37: 11 residues within 4Å: Chain C: Q.54, L.58, P.59, N.60, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.38: 11 residues within 4Å: Chain C: N.33, R.37, E.39, H.51, W.53, Q.103, D.107, T.108, N.109, W.111 Ligands: GOL.42 Ligand excluded by PLIP GOL.39: 10 residues within 4Å: Chain C: N.130, R.134, E.136, H.148, W.150, Q.199, H.203, T.204, D.205, W.207 Ligand excluded by PLIP GOL.40: 8 residues within 4Å: Chain C: N.178, R.182, E.184, H.196, W.198, Q.247, V.253, W.255 Ligand excluded by PLIP GOL.41: 10 residues within 4Å: Chain C: N.82, R.86, E.88, H.100, W.102, Q.151, H.155, T.156, N.157, W.159 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain C: D.35, R.37, T.55, D.107 Ligands: GOL.38 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain C: T.74, S.75, R.92, A.365, S.366, V.367, I.368 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain C: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP GOL.46: 5 residues within 4Å: Chain A: N.257 Chain C: D.262, G.263, N.304, W.305 Ligand excluded by PLIP GOL.53: 11 residues within 4Å: Chain D: Q.54, L.58, P.59, N.60, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.54: 11 residues within 4Å: Chain D: N.33, R.37, E.39, H.51, W.53, Q.103, D.107, T.108, N.109, W.111 Ligands: GOL.58 Ligand excluded by PLIP GOL.55: 10 residues within 4Å: Chain D: N.130, R.134, E.136, H.148, W.150, Q.199, H.203, T.204, D.205, W.207 Ligand excluded by PLIP GOL.56: 8 residues within 4Å: Chain D: N.178, R.182, E.184, H.196, W.198, Q.247, V.253, W.255 Ligand excluded by PLIP GOL.57: 10 residues within 4Å: Chain D: N.82, R.86, E.88, H.100, W.102, Q.151, H.155, T.156, N.157, W.159 Ligand excluded by PLIP GOL.58: 5 residues within 4Å: Chain D: D.35, R.37, T.55, D.107 Ligands: GOL.54 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain D: T.74, S.75, R.92, A.365, S.366, V.367, I.368 Ligand excluded by PLIP GOL.60: 6 residues within 4Å: Chain D: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP GOL.62: 5 residues within 4Å: Chain B: N.257 Chain D: D.262, G.263, N.304, W.305 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gajdos, L. et al., Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Structure (2021)

Release Date

2021-03-17

Peptides

PLL lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

PLL lectin

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