SMTL ID : 3wmp.1

Crystal structure of SLL-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: N.60, S.62, D.64, H.74, N.76, W.78 Chain B: R.16 Ligands: CL.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.16, B:R.16 NAG-NAG.2: 8 residues within 4Å: Chain B: N.60, S.62, D.64, H.74, N.76, W.78 Chain C: R.16 Ligands: CL.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.16, C:R.16 NAG-NAG.3: 8 residues within 4Å: Chain A: R.16 Chain C: N.60, S.62, D.64, H.74, N.76, W.78 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.16, A:R.16 NAG-NAG.4: 8 residues within 4Å: Chain D: N.60, S.62, D.64, H.74, N.76, W.78 Chain F: R.16 Ligands: CL.28 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.64 NAG-NAG.5: 8 residues within 4Å: Chain D: R.16 Chain E: N.60, S.62, D.64, H.74, N.76, W.78 Ligands: CL.21 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.16, D:R.16 NAG-NAG.6: 8 residues within 4Å: Chain E: R.16 Chain F: N.60, S.62, D.64, H.74, N.76, W.78 Ligands: CL.24 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.16

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 7 residues within 4Å: Chain A: N.56, R.58, W.78 Chain B: W.18, D.50, W.84, N.85 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.18, B:W.84 Hydrogen bonds: B:D.50, A:N.56, A:R.58, A:W.78 MPD.15: 6 residues within 4Å: Chain A: W.18, D.50, W.84 Chain C: N.56, R.58, W.78 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.56, C:R.58, C:W.78, A:D.50 Hydrophobic interactions: A:W.18, A:W.84 MPD.19: 7 residues within 4Å: Chain D: W.18, D.50, W.84, N.85 Chain E: N.56, R.58, W.78 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:W.18, D:W.84 Hydrogen bonds: D:D.50, E:N.56, E:R.58, E:W.78

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 4 residues within 4Å: Chain A: N.55, N.56, R.58, T.80 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.16, M.48 Ligands: NAG-NAG.3 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: N.55, N.56, R.58, T.80 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.16, M.48 Ligands: NAG-NAG.1 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: N.55, N.56, R.58, T.80 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: T.14, R.16, M.48 Ligands: NAG-NAG.2 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: N.55, N.56, R.58, T.80 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain D: R.16, M.48 Ligands: NAG-NAG.5 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain E: N.55, N.56, R.58, T.80 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain E: R.16, M.48 Ligands: NAG-NAG.6 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain F: N.55, N.56, R.58, T.80 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain F: R.16, M.48 Ligands: NAG-NAG.4 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.10: 3 residues within 4Å: Chain A: H.15, C.17, D.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.15, A:D.23 NA.13: 3 residues within 4Å: Chain B: H.15, C.17, D.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.15, B:D.23, B:D.23 NA.18: 3 residues within 4Å: Chain C: H.15, C.17, D.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.15, C:D.23 Water bridges: C:Y.86 NA.22: 2 residues within 4Å: Chain D: H.15, C.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.15 Water bridges: D:Y.86 NA.25: 4 residues within 4Å: Chain E: H.15, C.17, C.22, D.23 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.15, E:D.23 NA.29: 3 residues within 4Å: Chain F: H.15, C.17, D.23 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.15, F:D.23, F:D.23

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.14: 7 residues within 4Å: Chain B: N.56, R.58, W.78, Y.79 Chain C: W.18, D.50, W.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.56, B:R.58, B:W.78 Salt bridges: B:R.58

1 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.26: 7 residues within 4Å: Chain D: N.56, R.58, W.78, Y.79 Chain F: W.18, D.50, W.84 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:N.56, D:R.58, D:W.78, F:W.84 Salt bridges: D:R.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kita, A. et al., Crystal structure of a symbiosis-related lectin from octocoral. Glycobiology (2015)

Release Date

2015-01-14

Peptides

Galactose-binding lectin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Galactose-binding lectin

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