SMTL ID : 5c9l.1

Crystal structure of native PLL lectin from Photorhabdus luminescens at 1.65 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

8 x HG: MERCURY (II) ION(Non-covalent)

HG.1: 4 residues within 4Å: Chain A: C.128, A.175, H.176 Ligands: CL.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.128, A:A.175 HG.2: 5 residues within 4Å: Chain A: H.298 Chain C: H.298 Ligands: HG.17, HG.32, HG.47 No protein-ligand interaction detected (PLIP) HG.16: 4 residues within 4Å: Chain B: C.128, A.175, H.176 Ligands: CL.20 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.128, B:A.175 HG.17: 5 residues within 4Å: Chain B: H.298 Chain D: H.298 Ligands: HG.2, HG.32, HG.47 No protein-ligand interaction detected (PLIP) HG.31: 4 residues within 4Å: Chain C: C.128, A.175, H.176 Ligands: CL.35 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.128, C:A.175 HG.32: 5 residues within 4Å: Chain A: H.298 Chain C: H.298 Ligands: HG.2, HG.17, HG.47 No protein-ligand interaction detected (PLIP) HG.46: 4 residues within 4Å: Chain D: C.128, A.175, H.176 Ligands: CL.50 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.128, D:A.175 HG.47: 5 residues within 4Å: Chain B: H.298 Chain D: H.298 Ligands: HG.2, HG.17, HG.32 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.132, H.203 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.132, A:H.203, A:H.203, H2O.8, H2O.11 CA.4: 3 residues within 4Å: Chain A: D.84, R.86, H.155 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.84, A:H.155, A:H.155, H2O.11, H2O.12 CA.18: 2 residues within 4Å: Chain B: D.132, H.203 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.132, B:H.203, B:H.203, H2O.23, H2O.26 CA.19: 3 residues within 4Å: Chain B: D.84, R.86, H.155 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.84, B:H.155, B:H.155, H2O.25, H2O.26 CA.33: 2 residues within 4Å: Chain C: D.132, H.203 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.132, C:H.203, C:H.203, H2O.37, H2O.40 CA.34: 3 residues within 4Å: Chain C: D.84, R.86, H.155 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.84, C:H.155, C:H.155, H2O.40, H2O.40 CA.48: 2 residues within 4Å: Chain D: D.132, H.203 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.132, D:H.203, D:H.203, H2O.51, H2O.54 CA.49: 3 residues within 4Å: Chain D: D.84, R.86, H.155 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.84, D:H.155, D:H.155, H2O.54, H2O.55

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

CL.5: 5 residues within 4Å: Chain A: E.126, V.127, C.128, A.175 Ligands: HG.1 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: E.126, V.127, C.128, A.175 Ligands: HG.16 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain C: E.126, V.127, C.128, A.175 Ligands: HG.31 Ligand excluded by PLIP CL.50: 5 residues within 4Å: Chain D: E.126, V.127, C.128, A.175 Ligands: HG.46 Ligand excluded by PLIP

8 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 7 residues within 4Å: Chain A: R.140, S.142, N.144, T.168, L.169, T.170, A.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.142, A:N.144, A:A.190 Water bridges: A:R.140 PG4.7: 8 residues within 4Å: Chain A: A.34, N.36, R.81, K.320, N.321 Chain B: N.130, S.131, L.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.36 Water bridges: A:R.81 PG4.21: 7 residues within 4Å: Chain B: R.140, S.142, N.144, T.168, L.169, T.170, A.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.142, B:N.144, B:A.190 Water bridges: B:R.140 PG4.22: 8 residues within 4Å: Chain A: N.130, S.131, L.177 Chain B: A.34, N.36, R.81, K.320, N.321 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.36 Water bridges: B:R.81 PG4.36: 7 residues within 4Å: Chain C: R.140, S.142, N.144, T.168, L.169, T.170, A.190 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.142, C:N.144, C:A.190 Water bridges: C:R.140 PG4.37: 8 residues within 4Å: Chain C: A.34, N.36, R.81, K.320, N.321 Chain D: N.130, S.131, L.177 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.36 Water bridges: C:R.81 PG4.51: 7 residues within 4Å: Chain D: R.140, S.142, N.144, T.168, L.169, T.170, A.190 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.142, D:N.144, D:A.190 Water bridges: D:R.140 PG4.52: 8 residues within 4Å: Chain C: N.130, S.131, L.177 Chain D: A.34, N.36, R.81, K.320, N.321 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.36 Water bridges: D:R.81

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

EDO.8: 5 residues within 4Å: Chain A: G.119, G.120, I.121, W.147, W.162 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: W.291, W.305 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: T.45, D.46 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: G.167, T.168, L.169, A.187, R.188, G.189, W.195, W.210 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: G.310, I.311, I.312, G.332, W.338, W.354 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: V.72, G.93, T.94, W.99 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: S.164, L.165, G.166 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: G.119, G.120, I.121, W.147, W.162 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: W.291, W.305 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: T.45, D.46 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain B: G.167, T.168, L.169, A.187, R.188, G.189, W.195, W.210 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: G.310, I.311, I.312, G.332, W.338, W.354 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: V.72, G.93, T.94, W.99 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: S.164, L.165, G.166 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain C: G.119, G.120, I.121, W.147, W.162 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain C: W.291, W.305 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain C: T.45, D.46 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain C: G.167, T.168, L.169, A.187, R.188, G.189, W.195, W.210 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain C: G.310, I.311, I.312, G.332, W.338, W.354 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain C: V.72, G.93, T.94, W.99 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain C: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain C: S.164, L.165, G.166 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain D: G.119, G.120, I.121, W.147, W.162 Ligand excluded by PLIP EDO.54: 2 residues within 4Å: Chain D: W.291, W.305 Ligand excluded by PLIP EDO.55: 2 residues within 4Å: Chain D: T.45, D.46 Ligand excluded by PLIP EDO.56: 8 residues within 4Å: Chain D: G.167, T.168, L.169, A.187, R.188, G.189, W.195, W.210 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain D: G.310, I.311, I.312, G.332, W.338, W.354 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain D: V.72, G.93, T.94, W.99 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain D: R.292, W.294, S.306, S.307, F.308, W.351 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain D: S.164, L.165, G.166 Ligand excluded by PLIP

Links

RCSB   PDBe   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