SMTL ID : 6f2p.1

Structure of Paenibacillus xanthan lyase to 2.6 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.490, D.491, E.492, Q.636, E.651 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.490, A:D.491, A:E.492, A:E.492, A:E.651 CA.2: 5 residues within 4Å: Chain A: E.769, E.771, S.791, K.794, D.894 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.769, A:E.771, A:S.791, A:K.794, A:D.894 CA.3: 3 residues within 4Å: Chain A: D.780, N.801, D.805 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.780, A:D.805, A:D.805 CA.4: 3 residues within 4Å: Chain A: D.329, D.331, T.333 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.329, A:D.331, A:T.333, H2O.14, H2O.17 CA.5: 3 residues within 4Å: Chain A: Q.161, S.163, E.174 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.163, A:E.174, H2O.1, H2O.4, H2O.9 CA.6: 5 residues within 4Å: Chain A: D.910, N.911, Y.933, D.936, D.1032 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.910, A:D.910, A:Y.933, A:D.936, A:D.1032 CA.7: 2 residues within 4Å: Chain A: G.946, D.1023 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.946, A:D.1023, H2O.16, H2O.18 CA.8: 1 residues within 4Å: Chain A: G.565 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.565, H2O.13 CA.9: 2 residues within 4Å: Chain A: A.206, Q.698 No protein-ligand interaction detected (PLIP)

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

CL.10: 2 residues within 4Å: Chain A: K.50 Ligands: BTB.14 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: V.784, K.794 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: W.58, N.59, D.60 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: T.167, A.169, N.170 Ligand excluded by PLIP

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.14: 5 residues within 4Å: Chain A: Q.42, W.45, D.46, K.50 Ligands: CL.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.42, A:W.45 Water bridges: A:D.46, A:K.50, A:K.50 pi-Cation interactions: A:W.45

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

MRD.15: 2 residues within 4Å: Chain A: N.546, A.632 Ligand excluded by PLIP MRD.16: 3 residues within 4Å: Chain A: Q.250, V.251, K.256 Ligand excluded by PLIP MRD.17: 5 residues within 4Å: Chain A: R.75, Y.78, A.133, D.136 Ligands: MPD.22 Ligand excluded by PLIP MRD.18: 3 residues within 4Å: Chain A: N.528, N.546, Y.547 Ligand excluded by PLIP MRD.19: 5 residues within 4Å: Chain A: S.151, Y.158, N.185 Ligands: MRD.20, MRD.34 Ligand excluded by PLIP MRD.20: 6 residues within 4Å: Chain A: Y.142, A.147, L.184, N.185, K.186 Ligands: MRD.19 Ligand excluded by PLIP MRD.21: 3 residues within 4Å: Chain A: D.664, N.839, L.874 Ligand excluded by PLIP MRD.23: 4 residues within 4Å: Chain A: N.789, A.790, S.791, R.824 Ligand excluded by PLIP MRD.26: 4 residues within 4Å: Chain A: L.991, L.1004, L.1005 Ligands: MPD.36 Ligand excluded by PLIP MRD.28: 5 residues within 4Å: Chain A: S.479, A.501, S.502, T.503 Ligands: MRD.40 Ligand excluded by PLIP MRD.30: 4 residues within 4Å: Chain A: T.713, L.715, S.750, T.754 Ligand excluded by PLIP MRD.31: 4 residues within 4Å: Chain A: D.431, Y.433, N.443, R.576 Ligand excluded by PLIP MRD.32: 2 residues within 4Å: Chain A: Y.965, K.1035 Ligand excluded by PLIP MRD.33: 4 residues within 4Å: Chain A: R.75, W.124, M.132, W.173 Ligand excluded by PLIP MRD.34: 5 residues within 4Å: Chain A: N.115, A.155, Y.158, Y.159 Ligands: MRD.19 Ligand excluded by PLIP MRD.40: 3 residues within 4Å: Chain A: T.611, S.644 Ligands: MRD.28 Ligand excluded by PLIP MRD.41: 6 residues within 4Å: Chain A: P.1, R.2, E.5, S.188, S.248, W.249 Ligand excluded by PLIP

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

MPD.22: 6 residues within 4Å: Chain A: Y.13, M.132, D.136, Q.176, D.239 Ligands: MRD.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.13 Hydrogen bonds: A:D.239 MPD.24: 2 residues within 4Å: Chain A: E.859, S.897 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.822 Water bridges: A:S.897 MPD.25: 3 residues within 4Å: Chain A: D.719, K.743, S.744 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.744 Water bridges: A:D.719, A:N.720 MPD.27: 6 residues within 4Å: Chain A: S.307, Q.308, K.319, A.345, Q.348, L.349 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.319, A:L.349 Hydrogen bonds: A:S.307, A:S.307 Water bridges: A:K.319, A:K.319 MPD.29: 4 residues within 4Å: Chain A: E.771, L.773, P.774, I.775 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.775 MPD.35: 1 residues within 4Å: Chain A: D.453 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.455 Water bridges: A:S.455, A:S.455, A:S.455, A:S.455 MPD.36: 6 residues within 4Å: Chain A: N.992, V.993, N.994, N.998, N.1003 Ligands: MRD.26 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.994, A:N.1003 Hydrogen bonds: A:N.992, A:N.994 Water bridges: A:N.1003 MPD.37: 4 residues within 4Å: Chain A: K.50, D.51, D.100, S.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.50, A:S.103 Water bridges: A:R.54 MPD.38: 6 residues within 4Å: Chain A: P.666, T.673, N.675, Y.705, D.707, P.870 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.673, A:N.675, A:Y.705, A:P.870 Water bridges: A:N.675, A:P.870 MPD.39: 6 residues within 4Å: Chain A: E.690, S.717, K.718, D.719, K.746, K.748 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.717, A:S.717

Links

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Citation

Jensen, P.F. et al., Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity. Cell Chem Biol (2019)

Release Date

2018-12-05

Peptides

Paenibacillus xanthan lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Paenibacillus xanthan lyase