SMTL ID : 6rgr.1

Photorhabdus asymbiotica lectin PHL in complex with L-rhamnose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: G.76, Q.77, W.104, W.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.77, A:Q.77 EDO.4: 5 residues within 4Å: Chain A: W.55, W.71, G.360, V.361, L.362 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.361 Water bridges: A:T.50 EDO.12: 4 residues within 4Å: Chain B: G.76, Q.77, W.104, W.118 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.77, B:Q.77 EDO.15: 5 residues within 4Å: Chain B: W.55, W.71, G.360, V.361, L.362 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.361 Water bridges: B:T.50

4 x RM4: beta-L-rhamnopyranose(Non-covalent)

RM4.2: 9 residues within 4Å: Chain A: N.182, R.186, E.188, H.200, W.202, Q.251, S.256, G.257, W.259 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.182, A:E.188, A:H.200, A:H.200, A:Q.251 Salt bridges: A:R.186 RM4.3: 10 residues within 4Å: Chain A: N.278, R.282, E.284, H.296, W.298, Q.347, T.348, S.350, S.351, W.352 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.278, A:E.284, A:H.296, A:H.296, A:Q.347, A:S.351 Salt bridges: A:R.282 RM4.13: 9 residues within 4Å: Chain B: N.182, R.186, E.188, H.200, W.202, Q.251, S.256, G.257, W.259 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.182, B:E.188, B:H.200, B:Q.251 Water bridges: B:E.215 Salt bridges: B:R.186 RM4.14: 10 residues within 4Å: Chain B: N.278, R.282, E.284, H.296, W.298, Q.347, T.348, S.350, S.351, W.352 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.278, B:E.284, B:H.296, B:Q.347, B:S.351 Salt bridges: B:R.282

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

NA.5: 6 residues within 4Å: Chain A: N.134, T.135, G.185, Q.203, P.206, D.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.135, A:D.207, A:D.207 NA.6: 4 residues within 4Å: Chain A: N.182, S.183, G.233, Q.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.182, A:S.183, A:L.235 NA.7: 4 residues within 4Å: Chain A: D.339, A.341, W.343, S.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.339, A:S.357 NA.8: 2 residues within 4Å: Chain A: T.178, V.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.178, A:V.179, A:V.179 NA.16: 6 residues within 4Å: Chain B: N.134, T.135, G.185, Q.203, P.206, D.207 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.135, B:Q.203, B:D.207, B:D.207 NA.17: 4 residues within 4Å: Chain B: N.182, S.183, G.233, Q.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.183, B:S.183, B:L.235 NA.18: 4 residues within 4Å: Chain B: D.339, A.341, W.343, S.357 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.357, B:S.357 NA.19: 2 residues within 4Å: Chain B: T.178, V.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.178, B:V.179 Water bridges: B:T.178

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

CL.9: 2 residues within 4Å: Chain A: S.213, W.214 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: P.67 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.240, T.270 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: S.213, W.214 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: P.67 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: R.240, T.270 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Fujdiarova, E. et al., Heptabladed beta-propeller lectins PLL2 and PHL from Photorhabdus spp. recognize O-methylated sugars and influence the host immune system. Febs J. (2020)

Release Date

2020-07-01

Peptides

Lectin PHL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lectin PHL

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