SMTL ID : 5mxh.1

Photorhabdus asymbiotica lectin (PHL) in complex with D-galactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

6 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.1: 11 residues within 4Å: Chain A: N.87, R.91, E.93, H.105, W.107, Q.119, Q.155, H.159, S.160, G.161, W.163 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.87, A:R.91, A:R.91, A:E.93, A:E.93, A:Q.119, A:Q.155, A:S.160, A:G.161 Salt bridges: A:H.105 GAL.2: 9 residues within 4Å: Chain A: N.182, R.186, E.188, H.200, W.202, Q.251, S.256, G.257, W.259 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.182, A:R.186, A:R.186, A:E.188, A:E.188, A:Q.251, A:S.256, A:G.257 Water bridges: A:E.215, A:G.257 Salt bridges: A:H.200 GAL.3: 7 residues within 4Å: Chain A: N.278, R.282, E.284, H.296, W.298, Q.347, W.352 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.278, A:N.278, A:R.282, A:R.282, A:E.284, A:Q.347 Salt bridges: A:H.296 GAL.9: 11 residues within 4Å: Chain B: N.87, R.91, E.93, H.105, W.107, Q.119, Q.155, H.159, S.160, G.161, W.163 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.87, B:R.91, B:R.91, B:E.93, B:E.93, B:Q.119, B:Q.155, B:S.160, B:G.161 Salt bridges: B:H.105 GAL.10: 9 residues within 4Å: Chain B: N.182, R.186, E.188, H.200, W.202, Q.251, S.256, G.257, W.259 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.182, B:R.186, B:R.186, B:E.188, B:E.188, B:Q.251, B:S.256, B:G.257 Water bridges: B:G.257 Salt bridges: B:H.200 GAL.11: 7 residues within 4Å: Chain B: N.278, R.282, E.284, H.296, W.298, Q.347, W.352 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.278, B:N.278, B:R.282, B:R.282, B:E.284, B:Q.347 Salt bridges: B:H.296

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: N.37, T.38 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.38, H2O.1, H2O.9, H2O.10, H2O.13 MG.12: 2 residues within 4Å: Chain B: N.37, T.38 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.38, H2O.2, H2O.11, H2O.20, H2O.20

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

CL.5: 6 residues within 4Å: Chain A: G.49, T.50, D.51, K.52, A.53, W.55 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: H.180, I.228, D.229, K.277 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: G.145, A.146, D.147, N.148, A.149, W.151 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.336, I.363, D.364 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: G.49, T.50, D.51, K.52, A.53, W.55 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: H.180, I.228, D.229, K.277 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: G.145, A.146, D.147, N.148, A.149, W.151 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: R.336, I.363, D.364 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Jancarikova, G. et al., Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity. PLoS Pathog. (2017)

Release Date

2017-08-09

Peptides

Photorhabdus asymbiotica lectin PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Photorhabdus asymbiotica lectin PHL

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