SMTL ID : 2z8r.3 (2 other biounits)

Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.2: 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.3: 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.17, H2O.17 CA.4: 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.5 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: 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.5 CA.7: 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.8: 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.1, H2O.4 CA.9: 6 residues within 4Å: Chain A: D.334, D.336, E.340, D.349, H.350 Ligands: CA.10 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.8 CA.10: 6 residues within 4Å: Chain A: D.332, D.334, D.336, K.338, E.340 Ligands: CA.9 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.17: 5 residues within 4Å: Chain B: D.116, N.555, I.556, A.557, N.559 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.116, B:N.555, B:A.557, H2O.28, H2O.29 CA.18: 5 residues within 4Å: Chain B: D.370, D.372, R.375, G.377, E.379 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.372, B:R.375, B:G.377, B:E.379, H2O.30 CA.19: 4 residues within 4Å: Chain B: H.326, H.362, D.364, E.385 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.326, B:H.362, B:D.364, B:E.385, H2O.43, H2O.43 CA.20: 6 residues within 4Å: Chain B: D.506, L.508, G.509, D.510, R.512, E.514 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.506, B:L.508, B:D.510, B:R.512, B:E.514 CA.21: 5 residues within 4Å: Chain B: D.420, D.422, Y.425, G.427, E.429 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.422, B:Y.425, B:G.427, B:E.429, H2O.29 CA.22: 4 residues within 4Å: Chain B: D.459, D.461, L.463, E.465 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.459, B:D.461, B:D.461, B:L.463, B:E.465 CA.23: 5 residues within 4Å: Chain B: D.185, D.187, D.189, K.191, E.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.185, B:D.187, B:D.189, B:K.191, B:E.193 CA.24: 5 residues within 4Å: Chain B: D.121, D.123, D.125, Q.127, E.129 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.121, B:D.123, B:D.125, B:Q.127, B:E.129 CA.25: 6 residues within 4Å: Chain B: D.334, D.336, E.340, D.349, H.350 Ligands: CA.26 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.334, B:D.336, B:E.340, B:D.349, B:H.350, H2O.35 CA.26: 6 residues within 4Å: Chain B: D.332, D.334, D.336, K.338, E.340 Ligands: CA.25 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.332, B:D.334, B:D.336, B:K.338, B:E.340

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

MPD.11: 4 residues within 4Å: Chain A: S.85, W.87, H.92, Q.127 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.87 Hydrogen bonds: A:W.87 Water bridges: A:S.85 MPD.12: 6 residues within 4Å: Chain A: N.167, K.170, G.201, K.203, V.209, A.213 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.209 Hydrogen bonds: A:K.170, A:A.213 Water bridges: A:N.167, A:K.203, A:N.214 MPD.13: 5 residues within 4Å: Chain A: S.143, N.263, R.264, R.267, Y.289 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.289, A:Y.289 Hydrogen bonds: A:N.263, A:N.263, A:R.267 Water bridges: A:D.141, A:S.143 MPD.14: 1 residues within 4Å: Chain A: E.220 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.220, A:E.220 MPD.15: 2 residues within 4Å: Chain A: K.440, V.442 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.440, A:V.442 MPD.16: 5 residues within 4Å: Chain A: D.332, V.333, D.370, G.377, L.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.565 Water bridges: A:D.370, A:G.377 MPD.27: 4 residues within 4Å: Chain B: N.263, R.264, R.267, Y.289 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.289, B:Y.289 Hydrogen bonds: B:N.263, B:N.263, B:R.267 Water bridges: B:S.143, B:S.143 MPD.28: 4 residues within 4Å: Chain B: V.13, W.87, H.92, Q.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.87 MPD.29: 6 residues within 4Å: Chain B: I.210, G.211, Y.230, T.244, A.245, N.246 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.210, B:Y.230, B:Y.230 Water bridges: B:G.211, B:T.244, B:T.244 MPD.30: 5 residues within 4Å: Chain B: N.167, K.170, G.201, V.209, A.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.213 Water bridges: B:N.167, B:K.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ochiai, A. et al., A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER. J.Biol.Chem. (2007)

Release Date

2007-10-16

Peptides

YesW protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

YesW protein

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