SMTL ID : 5xqj.2 (3 other biounits)

Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

1 x RAM- GAD: 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose(Non-covalent)

RAM-GAD.1: 14 residues within 4Å: Chain A: L.433, Y.437, D.439, E.566, R.613, H.614, A.623, Q.625, R.627, P.666, Q.667, V.670, H.761, L.762 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.613, A:D.439, A:Q.625, A:R.627, A:R.627, A:Q.667 Salt bridges: A:R.613, A:H.614, A:R.627, A:R.613 Hydrophobic interactions: A:V.670

1 x RAM- GAD- GAL: 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-[beta-D-galactopyranose-(1-4)]alpha-L-rhamnopyranose

RAM-GAD-GAL.2: 16 residues within 4Å: Chain A: R.288 Chain B: Y.437, D.439, E.566, R.613, H.614, A.623, Q.625, R.627, P.666, Q.667, V.670, T.689, S.760, H.761, L.762 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.762, B:V.670 Hydrogen bonds: B:Y.437, B:R.613, A:R.288, B:R.613, B:Q.625, B:R.627, B:R.627, B:Q.625, B:Q.625, B:R.627, B:Q.667, B:T.689 Water bridges: B:E.566, B:E.566 Salt bridges: B:R.613, B:H.614, B:R.627

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.541, N.564, H.595, D.600, H.618 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.541, A:H.595, A:D.600, A:D.600, A:H.618 CA.4: 5 residues within 4Å: Chain B: D.541, N.564, H.595, D.600, H.618 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.541, B:H.595, B:D.600, B:D.600, B:H.618

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunishige, Y. et al., Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26. FEBS Lett. (2018)

Release Date

2018-04-04

Peptides

Pcrglx protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Pcrglx protein

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