SMTL ID : 7jwf.2 (1 other biounit)

Crystal structure of PdGH110B D344N in complex with alpha-(1,3)-galactobiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x GAL- GLA: alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose(Non-covalent)

GAL-GLA.1: 18 residues within 4Å: Chain A: N.85, R.208, R.265, M.291, D.321, H.324, N.344, D.345, N.348, R.451, A.452, R.453, L.456, E.480, W.486, E.488, W.510 Ligands: IOD.43 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.265, A:N.344, A:N.344, A:R.451, A:R.451, A:W.510, A:N.85, A:R.265, A:R.265, A:D.321, A:N.348, A:R.453, A:E.480 Water bridges: A:R.453, A:D.345, A:R.453, A:E.480 Salt bridges: A:R.208, A:R.451 GAL-GLA.52: 18 residues within 4Å: Chain B: N.85, R.208, R.265, M.291, D.321, H.324, N.344, D.345, N.348, R.451, A.452, R.453, L.456, E.480, W.486, E.488, W.510 Ligands: CL.96 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.265, B:N.344, B:N.344, B:R.451, B:R.451, B:N.85, B:N.85, B:R.265, B:R.265, B:D.321, B:N.348, B:R.453, B:R.453, B:E.480 Water bridges: B:D.225, B:H.324 Salt bridges: B:R.208, B:R.451

3 x MLT: D-MALATE(Non-covalent)

MLT.2: 4 residues within 4Å: Chain A: I.168, N.169, E.170 Chain B: F.227 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.169 Hydrogen bonds: A:E.170 Water bridges: A:A.171 MLT.50: 5 residues within 4Å: Chain A: H.390, I.395, Y.397, R.424, F.525 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.397 Hydrogen bonds: A:Y.397, A:Y.397 Salt bridges: A:H.390, A:R.424 MLT.54: 3 residues within 4Å: Chain B: D.190, R.191, R.194 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.191 Water bridges: B:R.191 Salt bridges: B:R.191, B:R.194

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: K.363, V.403, Q.416, F.417, I.418 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: K.304 Ligands: IOD.24 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: T.528, S.529, R.530 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: E.201 Chain B: K.207, F.227, G.229, N.230, K.263 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: H.286, P.310, S.311, K.312 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: G.154, P.248 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: L.237, N.238, D.241, V.242 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: R.217, P.310, E.340, S.341, K.449 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: S.493, K.533, N.534 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: A.151, G.152 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: I.592, S.593, I.594 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain B: K.498, K.538, G.539, N.563 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain B: I.584, I.590, P.611 Ligands: IOD.86 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain B: R.448, Y.469, H.471 Ligand excluded by PLIP EDO.58: 3 residues within 4Å: Chain B: I.592, S.593, I.594 Ligand excluded by PLIP EDO.59: 2 residues within 4Å: Chain B: K.66, N.109 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain B: M.81, Y.82, Q.296, R.297, G.376 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain B: H.390, I.395, Y.397, R.424 Ligand excluded by PLIP EDO.62: 1 residues within 4Å: Chain B: F.181 Ligand excluded by PLIP EDO.63: 4 residues within 4Å: Chain B: A.149, D.157, K.159, V.242 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain B: R.460, G.491, V.492, R.530, Y.531, K.533 Ligand excluded by PLIP EDO.65: 7 residues within 4Å: Chain A: T.44, H.45, Y.48, R.75, A.77 Chain B: R.407, V.408 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain B: R.217, P.310, E.340, S.341, K.449 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain B: H.286, S.311, K.312 Ligand excluded by PLIP

59 x IOD: IODIDE ION(Non-functional Binders)

IOD.14: 4 residues within 4Å: Chain A: R.297, N.327, F.379, K.433 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain A: K.207, R.208, F.227 Ligands: IOD.23 Ligand excluded by PLIP IOD.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: K.577 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: K.66, N.108 Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain A: K.55, S.99, F.100, N.101 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: R.68, H.115, S.139 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: H.371, Q.373 Chain B: K.195 Ligand excluded by PLIP IOD.22: 2 residues within 4Å: Chain A: I.594, S.606 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain A: F.227 Ligands: IOD.15 Ligand excluded by PLIP IOD.24: 2 residues within 4Å: Chain A: K.443 Ligands: EDO.4 Ligand excluded by PLIP IOD.25: 4 residues within 4Å: Chain A: C.328, I.349, R.435, A.438 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: R.575, K.577 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain A: T.404, T.406, R.414 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain A: K.153 Ligand excluded by PLIP IOD.29: 6 residues within 4Å: Chain A: R.79, I.93, P.96, L.97, S.98, I.122 Ligand excluded by PLIP IOD.30: 2 residues within 4Å: Chain A: S.587, I.590 Ligand excluded by PLIP IOD.31: 1 residues within 4Å: Chain A: F.33 Ligand excluded by PLIP IOD.32: 2 residues within 4Å: Chain A: R.233, F.246 Ligand excluded by PLIP IOD.33: 3 residues within 4Å: Chain A: D.162, Q.163 Ligands: MLA.46 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain A: K.401 Ligand excluded by PLIP IOD.35: 2 residues within 4Å: Chain A: K.426, E.427 Ligand excluded by PLIP IOD.36: 3 residues within 4Å: Chain A: T.329, R.435, S.436 Ligand excluded by PLIP IOD.37: 2 residues within 4Å: Chain A: R.92 Chain B: N.410 Ligand excluded by PLIP IOD.38: 3 residues within 4Å: Chain A: T.406, R.414 Chain B: H.45 Ligand excluded by PLIP IOD.39: 2 residues within 4Å: Chain A: F.601, S.602 Ligand excluded by PLIP IOD.40: 3 residues within 4Å: Chain A: K.207, F.227, K.263 Ligand excluded by PLIP IOD.41: 1 residues within 4Å: Chain A: I.168 Ligand excluded by PLIP IOD.42: 3 residues within 4Å: Chain A: N.499, K.538, G.539 Ligand excluded by PLIP IOD.43: 4 residues within 4Å: Chain A: K.207, R.208, R.265 Ligands: GAL-GLA.1 Ligand excluded by PLIP IOD.44: 4 residues within 4Å: Chain A: K.331, K.333, I.441 Ligands: MLI.47 Ligand excluded by PLIP IOD.45: 2 residues within 4Å: Chain A: D.523, K.524 Ligand excluded by PLIP IOD.68: 4 residues within 4Å: Chain B: R.297, N.327, F.379, K.433 Ligand excluded by PLIP IOD.69: 1 residues within 4Å: Chain B: F.33 Ligand excluded by PLIP IOD.70: 3 residues within 4Å: Chain B: R.208, F.227 Ligands: IOD.80 Ligand excluded by PLIP IOD.71: 1 residues within 4Å: Chain B: K.304 Ligand excluded by PLIP IOD.72: 1 residues within 4Å: Chain B: E.427 Ligand excluded by PLIP IOD.73: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.74: 3 residues within 4Å: Chain A: K.195, Q.199 Chain B: Q.373 Ligand excluded by PLIP IOD.75: 2 residues within 4Å: Chain B: R.68, S.139 Ligand excluded by PLIP IOD.76: 1 residues within 4Å: Chain B: K.577 Ligand excluded by PLIP IOD.77: 2 residues within 4Å: Chain B: D.523, K.524 Ligand excluded by PLIP IOD.78: 2 residues within 4Å: Chain B: R.575, K.577 Ligand excluded by PLIP IOD.79: 1 residues within 4Å: Chain B: P.248 Ligand excluded by PLIP IOD.80: 2 residues within 4Å: Chain B: D.225 Ligands: IOD.70 Ligand excluded by PLIP IOD.81: 4 residues within 4Å: Chain B: C.328, I.349, R.435, A.438 Ligand excluded by PLIP IOD.82: 3 residues within 4Å: Chain B: T.404, T.406, R.414 Ligand excluded by PLIP IOD.83: 2 residues within 4Å: Chain A: H.45 Chain B: R.414 Ligand excluded by PLIP IOD.84: 5 residues within 4Å: Chain B: R.79, I.93, P.96, S.98, I.122 Ligand excluded by PLIP IOD.85: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.86: 3 residues within 4Å: Chain B: S.587, I.590 Ligands: EDO.56 Ligand excluded by PLIP IOD.87: 1 residues within 4Å: Chain B: I.168 Ligand excluded by PLIP IOD.88: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.89: 2 residues within 4Å: Chain A: N.410 Chain B: R.92 Ligand excluded by PLIP IOD.90: 3 residues within 4Å: Chain B: T.329, R.435, S.436 Ligand excluded by PLIP IOD.91: 2 residues within 4Å: Chain B: D.162, Q.163 Ligand excluded by PLIP IOD.92: 1 residues within 4Å: Chain B: S.602 Ligand excluded by PLIP IOD.93: 3 residues within 4Å: Chain B: K.401, I.418, K.419 Ligand excluded by PLIP IOD.94: 3 residues within 4Å: Chain B: I.594, K.605, S.606 Ligand excluded by PLIP

1 x MLA: MALONIC ACID(Non-covalent)

MLA.46: 5 residues within 4Å: Chain A: S.139, Q.163, K.312, R.314 Ligands: IOD.33 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.163 Hydrogen bonds: A:Q.163 Salt bridges: A:K.312, A:R.314

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.47: 5 residues within 4Å: Chain A: K.333, I.441, K.443, L.464 Ligands: IOD.44 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.441, A:K.443 Salt bridges: A:K.333, A:K.443, A:K.443

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.48: 4 residues within 4Å: Chain A: K.153, Y.155, R.244, F.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.244, A:R.244 Water bridges: A:G.154

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.49: 4 residues within 4Å: Chain A: H.390, A.392, K.524, F.525 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.524 Water bridges: A:A.392 Salt bridges: A:H.390

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.51: 2 residues within 4Å: Chain A: N.552, Y.615 Ligand excluded by PLIP CL.95: 3 residues within 4Å: Chain B: K.55, F.100, N.101 Ligand excluded by PLIP CL.96: 4 residues within 4Å: Chain B: K.207, R.208, R.265 Ligands: GAL-GLA.52 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.53: 2 residues within 4Å: Chain B: D.523, K.524 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGuire, B.E. et al., The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of alpha-1,3-galactosidic linkages in lambda-carrageenan and blood group antigens. J.Biol.Chem. (2020)

Release Date

2020-11-04

Peptides

Glycoside hydrolase family 110: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

Glycoside hydrolase family 110

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