SMTL ID : 4fus.1

The X-ray structure of Hahella chejuensis family 48 glycosyl hydrolase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BGC.1: 13 residues within 4Å: Chain A: H.55, E.63, A.64, E.74, W.438, W.441, W.444, D.520, R.639, W.641 Ligands: PEG.2, GOL.4, ACT.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.55, A:H.55, A:E.74 Water bridges: A:Y.430, A:Y.430

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

PEG.2: 7 residues within 4Å: Chain A: Y.430, S.435, W.438, W.441 Ligands: BGC-BGC.1, BGC-BGC.1, GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.430

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.40, F.47, G.51, F.79, N.98, K.102 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.98 Water bridges: A:K.102, A:K.102 GOL.4: 9 residues within 4Å: Chain A: V.62, E.63, V.205, W.206, P.433, R.575, D.577 Ligands: BGC-BGC.1, PEG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.206 Water bridges: A:E.63 GOL.5: 7 residues within 4Å: Chain A: W.171, T.242, N.243, A.244, W.321, Y.322, Y.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.321, A:Y.348 Water bridges: A:W.171 GOL.6: 5 residues within 4Å: Chain A: A.126, S.127, Y.295, F.337 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.127, A:S.127, A:Y.295 GOL.7: 4 residues within 4Å: Chain A: S.127, W.335, F.337 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.127

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain A: W.560, T.561, K.564 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.560 Water bridges: A:K.564, A:K.564 Salt bridges: A:K.564 PO4.9: 4 residues within 4Å: Chain A: Y.586, P.588, G.589, E.590 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.586, A:G.589 Water bridges: A:Y.586, A:V.587, A:S.603

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

ACT.10: 4 residues within 4Å: Chain A: P.470, L.473, S.474, E.547 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.470 ACT.11: 5 residues within 4Å: Chain A: T.376, K.379, R.380, E.383, Y.420 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.376 Hydrogen bonds: A:Y.420 Salt bridges: A:R.380 ACT.12: 5 residues within 4Å: Chain A: A.64, T.72, E.74, W.171 Ligands: BGC-BGC.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.64, A:T.72, A:W.171 ACT.13: 5 residues within 4Å: Chain A: T.160, Y.161, G.162 Ligands: EDO.18, CA.26 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.366, A:R.366

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

EDO.14: 9 residues within 4Å: Chain A: Y.317, L.318, M.319, Q.349, N.350, A.354, W.374, G.377, S.381 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.317, A:M.319, A:N.350, A:N.350 EDO.15: 7 residues within 4Å: Chain A: Y.85, K.88, W.257, W.261, N.652, A.655 Ligands: EDO.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.85, A:Y.85 Water bridges: A:K.88 EDO.16: 7 residues within 4Å: Chain A: P.109, Q.111, Q.114, D.165, V.166, Y.167 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.165 Water bridges: A:Q.111 EDO.17: 7 residues within 4Å: Chain A: Y.161, S.163, D.165, Y.167, K.282, Y.286 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.165, A:K.282, A:Y.286 EDO.18: 2 residues within 4Å: Chain A: G.162 Ligands: ACT.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.162 EDO.19: 5 residues within 4Å: Chain A: P.122, S.123, E.150, D.151, A.155 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.123, A:E.150, A:E.150, A:A.155 EDO.20: 3 residues within 4Å: Chain A: A.155, K.156, Q.159 No protein-ligand interaction detected (PLIP) EDO.21: 10 residues within 4Å: Chain A: Y.85, Q.253, W.257, W.261, Q.447, E.451, F.533, N.652 Ligands: EDO.15, EDO.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.253, A:Q.447, A:N.652 Water bridges: A:N.652 EDO.22: 8 residues within 4Å: Chain A: Y.78, L.81, R.250, Q.253, Q.447, K.529, E.645 Ligands: EDO.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.253, A:Q.447, A:K.529, A:E.645 EDO.23: 7 residues within 4Å: Chain A: A.535, E.539, P.544, Q.545, N.546, K.549, F.657 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.539, A:E.539, A:Q.545, A:Q.545 EDO.24: 4 residues within 4Å: Chain A: F.419, Y.420, W.499, P.501 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.420 Water bridges: A:G.421, A:G.421, A:W.499 EDO.25: 8 residues within 4Å: Chain A: E.34, M.35, K.38, W.560, K.564, T.565, G.568, L.569 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.34, A:T.565, A:G.568 Water bridges: A:K.38

1 x CA: CALCIUM ION(Non-covalent)

CA.26: 2 residues within 4Å: Chain A: Q.159 Ligands: ACT.13 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.159, H2O.2, H2O.17

2 x NA: SODIUM ION(Non-functional Binders)

NA.27: 5 residues within 4Å: Chain A: E.104, E.105, I.108, T.110, M.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.104 NA.28: 3 residues within 4Å: Chain A: Q.202, E.207, D.432 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.202, A:D.432

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sukharnikov, L.O. et al., Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48. J.Biol.Chem. (2012)

Release Date

2012-10-17

Peptides

RTX toxins and related Ca2+-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RTX toxins and related Ca2+-binding protein