SMTL ID : 5axg.1

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: E.419, K.422, S.461, S.463 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.461, A:S.461, A:S.463 Water bridges: A:S.461, A:S.463 Salt bridges: A:K.422 PO4.2: 2 residues within 4Å: Chain A: R.416, L.539 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.416 PO4.3: 5 residues within 4Å: Chain A: Y.188, K.189, K.192, K.247, D.248 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.196 Salt bridges: A:K.189, A:K.192, A:K.247 PO4.4: 4 residues within 4Å: Chain A: N.267, H.268, P.269, R.317 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.267, A:N.267 Salt bridges: A:H.268, A:R.317 PO4.5: 2 residues within 4Å: Chain A: R.507, E.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.531 Salt bridges: A:R.507 PO4.12: 4 residues within 4Å: Chain B: N.267, H.268, P.269, R.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.267 Salt bridges: B:H.268, B:R.317 PO4.13: 2 residues within 4Å: Chain B: R.507, E.531 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.507 PO4.14: 7 residues within 4Å: Chain A: F.332, N.361 Chain B: H.382, S.505, A.506, V.532, S.533 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.506, B:S.533 Water bridges: B:H.382, B:S.505, A:N.361 Salt bridges: B:H.382

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

EDO.6: 9 residues within 4Å: Chain A: Y.235, H.310, D.312, N.352, Y.372, E.374, A.406, Y.408, F.453 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.310, A:N.352, A:E.374, A:Y.408 EDO.7: 3 residues within 4Å: Chain A: E.223, H.226, N.305 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.305 EDO.8: 7 residues within 4Å: Chain A: R.53, Y.55, H.226, N.229, I.230, M.231, D.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.53, A:Y.55, A:Y.55, A:H.226 EDO.9: 5 residues within 4Å: Chain A: K.148, G.399, K.400, A.402, R.483 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.483 Water bridges: A:K.148, A:K.400 EDO.15: 9 residues within 4Å: Chain B: Y.235, H.310, D.312, N.352, Y.372, E.374, A.406, Y.408, F.453 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.310, B:N.352, B:Y.372, B:E.374, B:Y.408 EDO.16: 6 residues within 4Å: Chain B: K.148, G.399, K.400, K.401, A.402, R.483 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.483 Water bridges: B:S.147, B:K.148, B:K.400 EDO.17: 5 residues within 4Å: Chain B: K.492, I.493, N.502, T.511, Y.512 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.493, B:T.511 Water bridges: B:I.493, B:A.513 EDO.18: 4 residues within 4Å: Chain B: Y.188, K.189, K.192, D.248 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.188, B:K.192, B:D.248 Water bridges: B:Y.188, B:G.196 EDO.19: 4 residues within 4Å: Chain B: K.422, S.461, E.462, S.463 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.422, B:S.461, B:E.462, B:S.463

1 x K: POTASSIUM ION(Non-covalent)

K.10: 2 residues within 4Å: Chain B: N.200, P.201 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.201, H2O.31

1 x CXS: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID(Non-covalent)

CXS.11: 7 residues within 4Å: Chain B: N.355, W.376, P.377, P.378, A.379, Y.411, E.451 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.376 Hydrogen bonds: B:N.355, B:A.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, N. et al., Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus. J.Biochem. (2016)

Release Date

2015-11-11

Peptides

Dextranase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dextranase