SMTL ID : 2zux.2 (1 other biounit)

Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

monomer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: H.326, H.362, D.364, E.385 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.326, A:H.362, A:D.364, A:E.385, H2O.9, H2O.11 CA.2: 5 residues within 4Å: Chain A: D.116, N.555, I.556, A.557, N.559 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.116, A:N.555, A:A.557, H2O.10, H2O.26 CA.3: 5 residues within 4Å: Chain A: D.420, D.422, Y.425, G.427, E.429 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.422, A:Y.425, A:G.427, A:E.429, H2O.2 CA.4: 5 residues within 4Å: Chain A: D.370, D.372, R.375, G.377, E.379 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.372, A:R.375, A:G.377, A:E.379, H2O.9 CA.5: 4 residues within 4Å: Chain A: D.459, D.461, L.463, E.465 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.459, A:D.461, A:D.461, A:L.463, A:E.465 CA.6: 6 residues within 4Å: Chain A: D.506, L.508, G.509, D.510, R.512, E.514 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.506, A:L.508, A:D.510, A:R.512, A:E.514 CA.7: 5 residues within 4Å: Chain A: D.121, D.123, D.125, Q.127, E.129 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.121, A:D.123, A:D.125, A:Q.127, A:E.129 CA.8: 5 residues within 4Å: Chain A: D.185, D.187, D.189, K.191, E.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.185, A:D.187, A:D.189, A:K.191, A:E.193 CA.9: 6 residues within 4Å: Chain A: D.332, D.334, D.336, K.338, E.340 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.332, A:D.334, A:D.336, A:K.338, A:E.340 CA.10: 6 residues within 4Å: Chain A: D.334, D.336, E.340, D.349, H.350 Ligands: CA.9 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.334, A:D.336, A:E.340, A:D.349, A:H.350, H2O.21

3 x RAM: alpha-L-rhamnopyranose(Non-covalent)

RAM.11: 5 residues within 4Å: Chain A: N.495, G.496, T.497, K.498, Y.558 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.497, A:T.497, A:Y.558 Water bridges: A:N.495 RAM.12: 6 residues within 4Å: Chain A: N.115, D.135, S.137, N.494, N.495, G.496 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.115, A:D.135, A:D.135, A:N.495, A:G.496 Water bridges: A:S.113, A:A.493, A:N.494, A:A.499, A:R.518 RAM.13: 6 residues within 4Å: Chain A: T.103, P.105, Y.110, D.150, K.170, R.218 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.218, A:R.218 Water bridges: A:D.150, A:N.167, A:K.170, A:K.170, A:K.170, A:K.170 Salt bridges: A:K.170

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

MPD.14: 6 residues within 4Å: Chain A: I.210, G.211, Y.230, T.244, A.245, N.246 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.210, A:Y.230, A:Y.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ochiai, A. et al., Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. J.Biol.Chem. (2009)

Release Date

2009-02-03

Peptides

YesW protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YesW protein

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