SMTL ID : 6htn.1 (1 other biounit)

Structure of a fucose lectin from Kordia zhangzhouensis in complex with methyl-fucoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

12 x MFU: methyl alpha-L-fucopyranoside(Non-covalent)

MFU.1: 10 residues within 4Å: Chain A: R.16, E.29, Y.38, G.40, A.41, L.42, I.64, I.66, W.82, W.87 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.64, A:I.66 Hydrogen bonds: A:E.29, A:A.41, A:L.42 Salt bridges: A:R.16 MFU.2: 10 residues within 4Å: Chain A: R.67, E.79, Y.88, G.90, A.91, L.92, I.114, I.116, W.132, W.137 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.114, A:I.116 Hydrogen bonds: A:R.67, A:E.79, A:A.91, A:L.92 Salt bridges: A:R.67 MFU.3: 9 residues within 4Å: Chain A: R.117, E.129, Y.138, G.140, A.141, Y.142 Chain B: L.15, W.32, W.37 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.129, A:A.141, A:Y.142 Water bridges: A:V.139 Salt bridges: A:R.117 Hydrophobic interactions: B:L.15 MFU.7: 10 residues within 4Å: Chain B: R.16, E.29, Y.38, G.40, A.41, L.42, I.64, I.66, W.82, W.87 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.64, B:I.66 Hydrogen bonds: B:R.16, B:E.29, B:A.41, B:L.42 Salt bridges: B:R.16 MFU.8: 10 residues within 4Å: Chain B: R.67, E.79, Y.88, G.90, A.91, L.92, I.114, I.116, W.132, W.137 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.114, B:I.116 Hydrogen bonds: B:R.67, B:E.79, B:A.91, B:L.92 Salt bridges: B:R.67 MFU.9: 11 residues within 4Å: Chain A: L.15, W.32, W.37 Chain B: R.117, E.129, C.131, Y.138, G.140, A.141, Y.142 Ligands: EDO.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.129, B:A.141, B:Y.142 Water bridges: B:V.139 Salt bridges: B:R.117 Hydrophobic interactions: A:L.15 MFU.12: 9 residues within 4Å: Chain C: R.16, E.29, G.40, A.41, L.42, I.64, I.66, W.82, W.87 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.64, C:I.66 Hydrogen bonds: C:E.29, C:A.41, C:L.42 Water bridges: C:Y.38 Salt bridges: C:R.16 MFU.13: 10 residues within 4Å: Chain C: R.67, E.79, Y.88, G.90, A.91, L.92, I.114, I.116, W.132, W.137 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.114, C:I.116 Hydrogen bonds: C:R.67, C:E.79, C:A.91, C:L.92 Water bridges: C:S.89 Salt bridges: C:R.67 MFU.14: 10 residues within 4Å: Chain C: R.117, E.129, Y.138, G.140, A.141, Y.142 Chain D: I.13, L.15, W.32, W.37 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.129, C:A.141, C:Y.142 Salt bridges: C:R.117 Hydrophobic interactions: D:I.13, D:L.15 MFU.18: 10 residues within 4Å: Chain D: R.16, E.29, Y.38, G.40, A.41, L.42, I.64, I.66, W.82, W.87 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.64, D:I.66 Hydrogen bonds: D:E.29, D:A.41, D:L.42 Water bridges: D:Y.38, D:D.39 Salt bridges: D:R.16 MFU.19: 10 residues within 4Å: Chain D: R.67, E.79, Y.88, G.90, A.91, L.92, I.114, I.116, W.132, W.137 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.114, D:I.116 Hydrogen bonds: D:R.67, D:E.79, D:A.91, D:L.92 Water bridges: D:S.89 Salt bridges: D:R.67 MFU.20: 9 residues within 4Å: Chain C: L.15, W.32, W.37 Chain D: R.117, E.129, Y.138, G.140, A.141, Y.142 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.129, D:A.141, D:Y.142 Water bridges: D:V.139 Salt bridges: D:R.117 Hydrophobic interactions: C:L.15

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 8 residues within 4Å: Chain A: S.100, D.103, Y.119, A.120, Y.121, Q.127 Chain B: I.17, S.19 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.119, A:Y.121, A:Q.127, B:I.17 Hydrogen bonds: A:D.103, A:Y.119 MRD.10: 8 residues within 4Å: Chain A: I.17, Y.18, S.19 Chain B: S.100, D.103, Y.119, Y.121, Q.127 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.17, B:Y.119, B:Y.121, B:Q.127 Water bridges: A:G.2, A:Y.18, B:D.103 Hydrogen bonds: B:Y.119 MRD.15: 8 residues within 4Å: Chain C: S.100, D.103, Y.119, A.120, Y.121, Q.127 Chain D: I.17, Y.18 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.119, C:Y.121, C:Q.127, D:I.17 Hydrogen bonds: C:D.103, C:Y.119 Water bridges: C:D.103 MRD.21: 9 residues within 4Å: Chain C: I.17, Y.18, S.19, G.51 Chain D: S.100, D.103, Y.119, Y.121, Q.127 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.17, D:Y.119, D:Y.121, D:Q.127 Hydrogen bonds: D:Y.119

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 3 residues within 4Å: Chain A: W.32 Chain B: A.141 Ligands: MFU.9 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: N.24, N.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.24 EDO.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain C: A.141, T.143 No protein-ligand interaction detected (PLIP)

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.11: 3 residues within 4Å: Chain B: D.85, K.86, Y.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.85, B:K.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonnardel, F. et al., Architecture and Evolution of Blade Assembly in beta-propeller Lectins. Structure (2019)

Release Date

2019-01-23

Peptides

Fucose-binding lectin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fucose-binding lectin

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