SMTL ID : 4jcm.1

Crystal structure of Gamma-CGTASE from Alkalophilic bacillus clarkii at 1.65 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.55, D.57, N.60, N.61, G.79, D.81 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.55, A:D.57, A:G.79, A:D.81, H2O.5 CA.2: 2 residues within 4Å: Chain A: Q.83, E.90 No protein-ligand interaction detected (PLIP) CA.3: 4 residues within 4Å: Chain A: A.175, Y.177, H.185 Ligands: GOL.35 No protein-ligand interaction detected (PLIP) CA.4: 1 residues within 4Å: Chain A: T.461 No protein-ligand interaction detected (PLIP) CA.5: 2 residues within 4Å: Chain A: Y.193, H.223 No protein-ligand interaction detected (PLIP) CA.6: 3 residues within 4Å: Chain A: N.164, I.209, H.252 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:I.209, A:H.252, H2O.2, H2O.2, H2O.6

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

CL.7: 2 residues within 4Å: Chain A: R.430, E.468 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: G.542, S.543 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: T.661, A.662 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.697 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: L.35, S.36, K.535 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: G.316 Ligand excluded by PLIP CL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: N.69 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: N.618 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: H.252 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: D.561, D.562 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: N.455 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain A: S.263, Y.266, D.267, G.528, D.532 Ligand excluded by PLIP

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

NA.20: 3 residues within 4Å: Chain A: G.256, V.655, S.656 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.656, A:S.656 Water bridges: A:G.256, A:K.259

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.21: 5 residues within 4Å: Chain A: Q.63, G.64, F.67, N.69 Ligands: EDO.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.64, A:N.69 SO4.22: 3 residues within 4Å: Chain A: E.90, T.149, H.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.90, A:E.90 Salt bridges: A:H.153 SO4.23: 3 residues within 4Å: Chain A: D.204, Y.205, H.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.205 Salt bridges: A:H.286 SO4.24: 3 residues within 4Å: Chain A: Y.322, K.428, E.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.322, A:Y.322, A:E.429 Water bridges: A:K.428 SO4.25: 3 residues within 4Å: Chain A: Y.383, T.403, T.404 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.404, A:T.404 Water bridges: A:T.357 SO4.26: 1 residues within 4Å: Chain A: N.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.492 SO4.27: 2 residues within 4Å: Chain A: Y.549, K.554 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.554 SO4.28: 2 residues within 4Å: Chain A: H.612, Y.648 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.648, A:Y.648 Salt bridges: A:H.612 SO4.29: 2 residues within 4Å: Chain A: Y.646, R.697 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.646, A:Y.646 Salt bridges: A:R.697 SO4.30: 2 residues within 4Å: Chain A: Y.474, H.475 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.472, A:H.475 Water bridges: A:H.475 Salt bridges: A:H.475 SO4.31: 3 residues within 4Å: Chain A: W.277, S.284, H.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.284, A:S.284 Water bridges: A:H.286 SO4.32: 1 residues within 4Å: Chain A: K.315 No protein-ligand interaction detected (PLIP) SO4.33: 3 residues within 4Å: Chain A: R.312, V.352, K.387 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.312, A:R.312, A:E.353 Salt bridges: A:R.312, A:K.387 SO4.34: 4 residues within 4Å: Chain A: G.386, K.387, G.391, K.394 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.387 Water bridges: A:K.394, A:K.394 Salt bridges: A:K.394

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.35: 4 residues within 4Å: Chain A: Y.177, L.182, H.185 Ligands: CA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.185 GOL.36: 3 residues within 4Å: Chain A: T.133, D.139, F.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.133, A:D.139, A:F.140 Water bridges: A:D.141 GOL.37: 3 residues within 4Å: Chain A: R.551, A.577, Q.578 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.578 GOL.38: 4 residues within 4Å: Chain A: W.631, K.666, W.678, N.683 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.683 GOL.39: 3 residues within 4Å: Chain A: H.510, S.512, E.513 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.510, A:E.513 GOL.40: 4 residues within 4Å: Chain A: K.231, Q.235, K.600, E.602 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.231, A:K.231, A:Q.235, A:K.600 Water bridges: A:Q.235 GOL.41: 2 residues within 4Å: Chain A: N.624, W.631 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.624, A:W.631 GOL.42: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.43: 6 residues within 4Å: Chain A: N.192, N.220, Q.222, H.223, R.605, T.695 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.192, A:N.220, A:T.695 Water bridges: A:Q.222, A:Q.222, A:Q.222, A:R.605, A:R.605, A:T.693, A:T.695, A:T.695, A:T.695

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

EDO.44: 2 residues within 4Å: Chain A: Y.615, G.616 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.616 EDO.45: 2 residues within 4Å: Chain A: K.490, E.491 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.491 Water bridges: A:N.492 EDO.46: 2 residues within 4Å: Chain A: K.535, T.564 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.535, A:T.564 Water bridges: A:K.535 EDO.47: 3 residues within 4Å: Chain A: G.64, Q.65 Ligands: SO4.21 No protein-ligand interaction detected (PLIP) EDO.48: 3 residues within 4Å: Chain A: H.319, N.433, D.434 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.434, A:D.434 EDO.49: 3 residues within 4Å: Chain A: R.355, D.356, V.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.356 EDO.50: 2 residues within 4Å: Chain A: Q.63, Q.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:Q.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, L. et al., The Crystal Structure of Gamma-Cgtase from Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution. To be Published

Release Date

2014-02-26

Peptides

Cyclodextrin glucanotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclodextrin glucanotransferase