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

Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: V.423, H.522 Ligands: GOL.22 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:V.423, A:H.522, H2O.29, H2O.29, H2O.29 CA.2: 3 residues within 4Å: Chain A: K.953 Ligands: GOL.21, GOL.23 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.953 CA.24: 2 residues within 4Å: Chain B: K.953 Ligands: GOL.46 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:K.953, H2O.61, H2O.68, H2O.68 CA.25: 3 residues within 4Å: Chain B: V.423, H.522 Ligands: GOL.47 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:V.423, B:H.522, H2O.61, H2O.61, H2O.61

43 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: Q.58, V.59, G.60, E.200, R.527 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: L.134, W.163, Y.497, V.498, P.500 Ligand excluded by PLIP GOL.5: 10 residues within 4Å: Chain A: L.223, F.262, G.265, V.266, R.267, V.303, I.305, S.314, H.315, F.316 Ligand excluded by PLIP GOL.6: 2 residues within 4Å: Chain A: Y.289, W.403 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: S.542, W.900 Chain B: L.545, G.829, R.833 Ligand excluded by PLIP GOL.8: 10 residues within 4Å: Chain A: D.567, E.572, W.576, D.579, W.629, E.841, R.858, H.862, W.864 Ligands: GOL.15 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: M.764, Q.797, I.798, Y.807, D.823, R.826, N.827 Ligands: GOL.12 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: T.279, E.280, W.281 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: Y.245, S.269, W.272, Y.364, R.365, P.368, E.369 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: I.798, R.826, N.827, Q.830, Y.843, F.846 Ligands: GOL.9 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: S.75, R.193, I.195, P.196, F.197 Chain B: E.425 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: E.201, Q.528, R.558 Chain B: Y.204, P.205, A.206 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain A: F.102, Q.147, E.572, W.576, W.679, W.684 Ligands: GOL.8 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: E.70, F.72, V.191, D.194, N.602 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: R.27, G.28, S.29, A.128, W.129 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain A: R.157, E.158, L.159 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain A: R.213, R.410, F.432, E.433, D.434 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain A: A.445, R.447, E.551, H.555 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: E.933, K.953, Y.954, M.955 Ligands: CA.2, GOL.23 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain A: V.423, P.424, H.522, E.523 Ligands: CA.1 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain A: V.952, K.953, Y.954 Chain B: R.409 Ligands: CA.2, GOL.21 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: Q.58, V.59, G.60, E.200, R.527 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain A: L.545, G.829, R.833 Chain B: S.542, W.900 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain B: L.134, W.163, Y.497, V.498 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain B: Q.797, I.798, N.827, Q.830, Y.843, F.846 Ligands: GOL.35 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain B: L.223, F.262, G.265, V.266, R.267, S.314, H.315, F.316 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain B: Y.289, W.403 Ligand excluded by PLIP GOL.32: 10 residues within 4Å: Chain B: D.567, E.572, W.576, D.579, W.629, E.841, R.858, H.862, W.864 Ligands: GOL.38 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain B: T.279, E.280, W.281 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain B: Y.245, S.269, Y.364, R.365, P.368, E.369 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain B: M.764, Q.797, I.798, Y.807, D.823, N.827 Ligands: GOL.29 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain A: E.425 Chain B: S.75, R.193, I.195, P.196, F.197 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain A: P.205, A.206 Chain B: E.201, Q.528, E.535, R.558 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain B: F.102, Q.147, E.572, W.576, W.622, W.684, N.849, R.858 Ligands: GOL.32 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain B: E.70, V.191, D.194, N.602 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain B: R.27, G.28, S.29, A.128, W.129, R.130 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain B: A.156, R.157, E.158, L.159, A.160, R.491 Ligand excluded by PLIP GOL.42: 5 residues within 4Å: Chain B: R.213, R.410, F.432, E.433, D.434 Ligand excluded by PLIP GOL.43: 3 residues within 4Å: Chain B: A.445, R.447, H.555 Ligand excluded by PLIP GOL.44: 7 residues within 4Å: Chain B: F.631, I.634, L.635, F.701, K.704, A.705, D.708 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain B: G.341, T.342, W.383, K.385 Ligand excluded by PLIP GOL.46: 5 residues within 4Å: Chain B: E.933, K.953, Y.954, M.955 Ligands: CA.24 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain B: V.423, P.424, R.494, H.522, E.523 Ligands: CA.25 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Z. et al., Crystal Structure of Glycoside Hydrolase Family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1. J.Mol.Biol. (2007)

Release Date

2007-11-13

Peptides

Rhamnosidase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Rhamnosidase B

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