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

C. bescii Family 3 pectate lyase double mutant K108A/Q111A in complex with trigalacturonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x X1X- ADA- ADA: alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-talopyranuronic acid

X1X-ADA-ADA.1: 20 residues within 4Å: Chain A: E.50, E.95, D.96, D.118, N.124, K.141, R.144, N.146, G.147, K.171 Ligands: CA.3, CA.4, CA.5, CA.6, ADA.11, ADA.12, ADA.13, GTR.14, ADA.15, ADA.16 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.50, A:N.124, A:D.118 Water bridges: A:E.50, A:E.50, A:D.96, A:K.101, A:N.146, A:N.146, A:K.141, A:K.141, 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

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 3 residues within 4Å: Chain A: D.92, V.93, E.115 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.92, A:V.93, A:E.115, H2O.3, H2O.5 CA.3: 8 residues within 4Å: Chain A: E.50, D.75, E.95, D.96 Ligands: X1X-ADA-ADA.1, CA.4, ADA.13, ADA.16 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.4 CA.4: 11 residues within 4Å: Chain A: E.50, E.95, D.96 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.3, CA.5, ADA.12, ADA.13, ADA.15, ADA.16 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.2 CA.5: 8 residues within 4Å: Chain A: Q.48, E.95, D.118 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.4, ADA.12, ADA.15 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.95, A:D.118, H2O.4, H2O.5, H2O.5 CA.6: 6 residues within 4Å: Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, ADA.11, ADA.12, GTR.14, ADA.15 No protein-ligand interaction detected (PLIP)

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

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

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

MRD.9: 4 residues within 4Å: Chain A: L.17, I.19, I.23, Y.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.31

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.10: 4 residues within 4Å: Chain A: N.164, V.165, K.166, N.188 No protein-ligand interaction detected (PLIP)

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

ADA.11: 10 residues within 4Å: Chain A: D.118, K.141, R.144, K.171 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.6, ADA.12, GTR.14, ADA.15 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.118 Water bridges: A:K.141, A:K.141, A:K.141, A:K.141, A:S.167, A:S.167 Salt bridges: A:K.141, A:K.141, A:R.144, A:K.171 ADA.12: 17 residues within 4Å: Chain A: E.50, E.95, D.118, R.144, N.146, G.147 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.4, CA.5, CA.6, ADA.11, ADA.13, GTR.14, ADA.15, ADA.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.50, A:G.147 Water bridges: A:G.147 ADA.13: 12 residues within 4Å: Chain A: E.50, E.95, D.96, N.124, N.146 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.3, CA.4, ADA.12, ADA.15, ADA.16 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.50, A:N.124 Water bridges: A:E.50, A:E.50, A:D.96, A:K.101, A:N.146 ADA.15: 17 residues within 4Å: Chain A: E.50, E.95, D.118, R.144, N.146, G.147 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.4, CA.5, CA.6, ADA.11, ADA.12, ADA.13, GTR.14, ADA.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.50, A:N.146, A:G.147 Water bridges: A:G.147 ADA.16: 12 residues within 4Å: Chain A: E.50, E.95, D.96, N.124, N.146 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.3, CA.4, ADA.12, ADA.13, ADA.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.50, A:N.124 Water bridges: A:E.50, A:E.50, A:D.96, A:K.101, A:N.146

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

GTR.14: 10 residues within 4Å: Chain A: D.118, K.141, R.144, K.171 Ligands: X1X-ADA-ADA.1, X1X-ADA-ADA.1, CA.6, ADA.11, ADA.12, ADA.15 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.118 Water bridges: A:D.118, A:D.118, A:K.141, A:K.141, A:K.141, A:S.167, A:S.167, A:S.167 Salt bridges: A:K.141, A:K.141, A:R.144, A:K.171

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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