SMTL ID : 5c9p.1

Crystal structure of recombinant PLL lectin complexed with L-fucose from Photorhabdus luminescens at 1.75 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

FUC.1: 7 residues within 4Å: Chain A: G.119, G.120, G.141, S.142, W.147, W.162 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.147, A:W.162 Hydrogen bonds: A:G.120, A:S.142, A:S.142 FUC.2: 7 residues within 4Å: Chain A: G.71, V.72, G.93, T.94, D.95, W.99, W.114 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.99, A:W.114 Hydrogen bonds: A:V.72, A:T.94, A:T.94, A:D.95 Water bridges: A:T.94, A:T.94 FUC.3: 8 residues within 4Å: Chain A: G.310, I.311, I.312, G.332, L.333, D.334, W.338, W.354 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.312 Hydrogen bonds: A:L.333, A:D.334 FUC.14: 7 residues within 4Å: Chain B: G.119, G.120, G.141, S.142, W.147, W.162 Ligands: GOL.26 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.147, B:W.162 Hydrogen bonds: B:G.120, B:S.142, B:S.142 FUC.15: 7 residues within 4Å: Chain B: G.71, V.72, G.93, T.94, D.95, W.99, W.114 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.99, B:W.114 Hydrogen bonds: B:V.72, B:T.94, B:T.94, B:D.95 Water bridges: B:T.94, B:T.94 FUC.16: 8 residues within 4Å: Chain B: G.310, I.311, I.312, G.332, L.333, D.334, W.338, W.354 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.312 Hydrogen bonds: B:L.333, B:D.334 FUC.27: 7 residues within 4Å: Chain C: G.119, G.120, G.141, S.142, W.147, W.162 Ligands: GOL.39 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.147, C:W.162 Hydrogen bonds: C:G.120, C:S.142, C:S.142 FUC.28: 7 residues within 4Å: Chain C: G.71, V.72, G.93, T.94, D.95, W.99, W.114 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.99, C:W.114 Hydrogen bonds: C:V.72, C:T.94, C:T.94, C:D.95 Water bridges: C:T.94, C:T.94 FUC.29: 8 residues within 4Å: Chain C: G.310, I.311, I.312, G.332, L.333, D.334, W.338, W.354 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.312 Hydrogen bonds: C:L.333, C:D.334 FUC.40: 7 residues within 4Å: Chain D: G.119, G.120, G.141, S.142, W.147, W.162 Ligands: GOL.52 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.147, D:W.162 Hydrogen bonds: D:G.120, D:S.142, D:S.142 FUC.41: 7 residues within 4Å: Chain D: G.71, V.72, G.93, T.94, D.95, W.99, W.114 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.99, D:W.114 Hydrogen bonds: D:V.72, D:T.94, D:T.94, D:D.95 Water bridges: D:T.94, D:T.94 FUC.42: 8 residues within 4Å: Chain D: G.310, I.311, I.312, G.332, L.333, D.334, W.338, W.354 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.312 Hydrogen bonds: D:L.333, D:D.334

40 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: Q.54, P.59, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.5: 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.6: 9 residues within 4Å: Chain A: N.82, R.86, E.88, H.100, W.102, Q.151, T.156, N.157, W.159 Ligand excluded by PLIP GOL.7: 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.9 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: R.292, W.294, S.306, S.307, F.308 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: D.35, R.37, T.55, D.107 Ligands: GOL.7 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: W.291, W.305, S.307 Ligand excluded by PLIP GOL.11: 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.12: 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.13: 4 residues within 4Å: Chain A: G.119, G.120, S.142 Ligands: FUC.1 Ligand excluded by PLIP GOL.17: 9 residues within 4Å: Chain B: Q.54, P.59, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.18: 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.19: 9 residues within 4Å: Chain B: N.82, R.86, E.88, H.100, W.102, Q.151, T.156, N.157, W.159 Ligand excluded by PLIP GOL.20: 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.22 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: R.292, W.294, S.306, S.307, F.308 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: D.35, R.37, T.55, D.107 Ligands: GOL.20 Ligand excluded by PLIP GOL.23: 3 residues within 4Å: Chain B: W.291, W.305, S.307 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: 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.26: 4 residues within 4Å: Chain B: G.119, G.120, S.142 Ligands: FUC.14 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain C: Q.54, P.59, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.31: 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.32: 9 residues within 4Å: Chain C: N.82, R.86, E.88, H.100, W.102, Q.151, T.156, N.157, W.159 Ligand excluded by PLIP GOL.33: 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.35 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain C: R.292, W.294, S.306, S.307, F.308 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain C: D.35, R.37, T.55, D.107 Ligands: GOL.33 Ligand excluded by PLIP GOL.36: 3 residues within 4Å: Chain C: W.291, W.305, S.307 Ligand excluded by PLIP GOL.37: 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.38: 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.39: 4 residues within 4Å: Chain C: G.119, G.120, S.142 Ligands: FUC.27 Ligand excluded by PLIP GOL.43: 9 residues within 4Å: Chain D: Q.54, P.59, S.61, W.63, N.321, R.325, E.327, H.339, W.341 Ligand excluded by PLIP GOL.44: 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.45: 9 residues within 4Å: Chain D: N.82, R.86, E.88, H.100, W.102, Q.151, T.156, N.157, W.159 Ligand excluded by PLIP GOL.46: 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.48 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain D: R.292, W.294, S.306, S.307, F.308 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain D: D.35, R.37, T.55, D.107 Ligands: GOL.46 Ligand excluded by PLIP GOL.49: 3 residues within 4Å: Chain D: W.291, W.305, S.307 Ligand excluded by PLIP GOL.50: 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.51: 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.52: 4 residues within 4Å: Chain D: G.119, G.120, S.142 Ligands: FUC.40 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure. J.Biol.Chem. (2016)

Release Date

2016-10-19

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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