SMTL ID : 4u6d.1

Zg3615, a family 117 glycoside hydrolase in complex with beta-3,6-anhydro-L-galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.63, D.374, S.376, V.379 Ligands: EDO.9 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.374, A:S.376, A:V.379, H2O.4, H2O.14 CA.2: 1 residues within 4Å: Chain A: P.90 No protein-ligand interaction detected (PLIP) CA.22: 1 residues within 4Å: Chain B: P.90 No protein-ligand interaction detected (PLIP) CA.23: 4 residues within 4Å: Chain B: E.63, D.374, S.376, V.379 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.63, B:S.376, B:V.379, H2O.20, H2O.21

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: R.301, N.329, H.354, F.355, T.356 Chain B: Y.390, F.391 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.301, A:T.356, A:T.356

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

EDO.4: 6 residues within 4Å: Chain A: Y.106, R.107, N.108, L.130, A.131, E.132 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: Y.100, D.140, F.142, W.350, R.370 Chain B: I.409, E.410 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: K.175, Y.177, Y.200 Ligands: EDO.12 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: N.53, Y.54, M.55, N.319, I.320, A.321 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: K.238, D.239, K.343 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: E.60, N.61, N.62, E.63, D.374, V.379, K.385 Ligands: CA.1 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: E.407, R.408, I.409 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: T.342, K.343, Y.344 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: Y.177, P.267 Ligands: EDO.6 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: W.172, K.173 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: F.76, D.77, Y.78, N.79, G.80, H.81 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: N.97, K.99, Y.101, D.205 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: K.36, Y.51, M.55 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: K.99, T.137, S.138, K.139, E.145 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: K.156, P.157, W.161 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: E.325, F.326 Chain B: E.325, F.326 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain A: Y.70, F.326, M.327, P.328, N.329, F.355 Chain B: Y.396 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: N.53, Y.54, M.55, N.319, I.320, A.321 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: T.71, K.74, F.142, T.143 Chain B: R.406 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: W.128, T.166, Q.181, F.183 Ligands: EDO.28 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: I.263, S.274, P.275, V.316 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: R.88, K.246, H.284, E.285, R.301 Ligands: EDO.26 Ligand excluded by PLIP

1 x 3DY: 3,6-anhydro-beta-L-galactopyranose(Non-covalent)

3DY.21: 12 residues within 4Å: Chain A: R.88, D.89, W.128, T.166, Q.181, D.192, H.230, D.231, K.246, H.284, E.285, H.354 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.181, A:H.230, A:K.246, A:H.284 Salt bridges: A:R.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ficko-Blean, E. et al., Biochemical and structural investigation of two paralogous glycoside hydrolases from Zobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-02-11

Peptides

Conserved hypothetical periplasmic protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Conserved hypothetical periplasmic protein