SMTL ID : 3wnk.1

Crystal Structure of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

10 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: D.647, Q.649, N.652 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.647, A:Q.649, H2O.2, H2O.4, H2O.4 CD.2: 3 residues within 4Å: Chain A: D.204, D.208 Ligands: ACT.15 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.204, A:D.208, H2O.5, H2O.11, ACT.15 CD.3: 1 residues within 4Å: Chain A: E.363 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.363, A:E.363, H2O.14, H2O.14, H2O.15 CD.4: 5 residues within 4Å: Chain A: E.407, E.409, T.426, G.429, D.524 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.407, A:E.409, A:T.426, A:G.429, A:D.524 CD.5: 3 residues within 4Å: Chain A: D.532, H.534, A.654 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.532, A:H.534, A:A.654, H2O.5, H2O.8 CD.6: 2 residues within 4Å: Chain A: G.140, E.145 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.145, A:E.145 CD.7: 2 residues within 4Å: Chain A: D.318, N.354 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.318, A:D.318, A:N.354 CD.8: 2 residues within 4Å: Chain A: E.136, R.568 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.136, A:E.136, H2O.7, H2O.14, H2O.17 CD.9: 3 residues within 4Å: Chain A: Y.398, H.562, E.563 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.398, A:E.563, H2O.14, H2O.14 CD.10: 1 residues within 4Å: Chain A: H.243 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.243

2 x CA: CALCIUM ION(Non-covalent)

CA.11: 1 residues within 4Å: Chain A: D.248 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.248, A:D.248, H2O.14, H2O.17, H2O.17 CA.12: 4 residues within 4Å: Chain A: N.415, Q.433, S.436, D.439 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.415, A:Q.433, A:D.439, H2O.9, H2O.13

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

NA.13: 2 residues within 4Å: Chain A: P.329, D.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.332 Water bridges: A:K.321, A:K.321 NA.14: 2 residues within 4Å: Chain A: V.30, A.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.30, A:V.30 Water bridges: A:A.116

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

ACT.15: 2 residues within 4Å: Chain A: D.208 Ligands: CD.2 No protein-ligand interaction detected (PLIP) ACT.16: 4 residues within 4Å: Chain A: H.67, R.101, N.592, D.634 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.101 Salt bridges: A:H.67, A:R.101

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 5 residues within 4Å: Chain A: N.421, H.422, D.432, W.489, N.522 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.421, A:N.522, A:N.522 Water bridges: A:D.432, A:Q.433, A:Q.433, A:N.522 GOL.18: 8 residues within 4Å: Chain A: Y.165, D.166, M.168, H.171, F.190, Y.216, M.218, Y.564 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, N. et al., Structural elucidation of the cyclization mechanism of alpha-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase. J.Biol.Chem. (2014)

Release Date

2014-02-05

Peptides

Cycloisomaltooligosaccharide glucanotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cycloisomaltooligosaccharide glucanotransferase