SMTL ID : 4yzq.1 (1 other biounit)

C. bescii Family 3 pectate lyase double mutant K108A/Q111N in complex with trigalacturonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x ADA- ADA- ADA: alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid

ADA-ADA-ADA.1: 17 residues within 4Å: Chain A: E.50, E.95, D.96, D.118, N.122, N.124, K.141, R.144, N.146, G.147, K.171 Ligands: CA.2, CA.3, CA.4, GTR.9, ADA.10, ADA.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.124, A:N.124 Water bridges: A:E.50, A:E.50, A:D.96, A:K.101

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: Q.48, E.50, E.95, D.118 Ligands: ADA-ADA-ADA.1, CA.3, ADA.10 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.95, A:D.118, H2O.3, H2O.4, H2O.4 CA.3: 9 residues within 4Å: Chain A: E.50, E.95, D.96 Ligands: ADA-ADA-ADA.1, ADA-ADA-ADA.1, CA.2, CA.4, ADA.10, ADA.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.50, A:E.50, A:E.95, A:E.95, H2O.3 CA.4: 6 residues within 4Å: Chain A: D.75, E.95, D.96 Ligands: ADA-ADA-ADA.1, CA.3, ADA.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.75, A:D.75, A:D.96, A:D.96, H2O.5 CA.5: 3 residues within 4Å: Chain A: D.92, V.93, E.115 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.92, A:E.115, H2O.2, H2O.3, H2O.7

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

MPD.6: 5 residues within 4Å: Chain A: T.128, K.130, Y.156, E.158, Y.204 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.128, A:Y.156, A:Y.156, A:Y.204 Water bridges: A:K.130 MPD.7: 3 residues within 4Å: Chain A: T.11, N.12, G.15 No protein-ligand interaction detected (PLIP) MPD.8: 4 residues within 4Å: Chain A: L.17, I.19, I.23, Y.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.31 Hydrogen bonds: A:Y.31

1 x GTR: beta-D-galactopyranuronic acid(Non-covalent)

GTR.9: 7 residues within 4Å: Chain A: D.118, K.141, R.144, K.171 Ligands: ADA-ADA-ADA.1, ADA-ADA-ADA.1, ADA.10 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.118 Water bridges: A:D.118, A:K.141, A:K.141, A:K.141, A:S.167 Salt bridges: A:K.141, A:K.141, A:R.144, A:K.171

2 x ADA: alpha-D-galactopyranuronic acid(Non-covalent)

ADA.10: 14 residues within 4Å: Chain A: E.50, E.95, D.118, N.122, R.144, N.146, G.147 Ligands: ADA-ADA-ADA.1, ADA-ADA-ADA.1, ADA-ADA-ADA.1, CA.2, CA.3, GTR.9, ADA.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.50, A:G.147 Water bridges: A:R.144 ADA.11: 11 residues within 4Å: Chain A: E.50, E.95, D.96, N.122, N.124, N.146 Ligands: ADA-ADA-ADA.1, ADA-ADA-ADA.1, CA.3, CA.4, ADA.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.124, A:N.124 Water bridges: A:E.50, A:E.50, A:D.96, A:K.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alahuhta, M. et al., The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-12-23

Peptides

Pectate lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pectate lyase

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