SMTL ID : 6kcx.1

Crystal structure of citrate complex of alpha-glucuronidase (TM0752)from Thermotoga maritima

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: C.193, N.221, H.222 Ligands: CIT.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:C.193, A:H.222, H2O.1, H2O.7, H2O.7 CO.6: 4 residues within 4Å: Chain B: C.193, N.221, H.222 Ligands: CIT.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.193, B:H.222, H2O.16, H2O.22, H2O.22

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 9 residues within 4Å: Chain A: I.18, G.19, M.49, D.50, V.51, L.82, A.96, P.98, L.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.50 IMD.7: 9 residues within 4Å: Chain B: I.18, G.19, M.49, D.50, V.51, L.82, A.96, P.98, L.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.50

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 7 residues within 4Å: Chain A: Y.124, W.286, Y.290, P.451, R.452 Chain B: T.453, K.454 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.286 Water bridges: B:T.453 IPA.8: 7 residues within 4Å: Chain A: T.453, K.454 Chain B: Y.124, W.286, Y.290, P.451, R.452 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.286 Water bridges: A:T.453

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 11 residues within 4Å: Chain A: V.135, S.136, T.137, N.172, H.222, W.257, D.279, R.282, R.311, F.314 Ligands: CO.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.135 Hydrogen bonds: A:N.172, A:D.279, A:R.282 Water bridges: A:R.311 Salt bridges: A:H.222, A:R.282, A:R.311 CIT.5: 8 residues within 4Å: Chain A: S.22, R.55, Y.97, S.106, G.107, S.108, L.318, R.322 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.97 Hydrogen bonds: A:S.106, A:S.106, A:S.106, A:S.108, A:R.322 Water bridges: A:S.22, A:V.23, A:R.24, A:R.55, A:R.319, A:R.322, A:R.322, A:R.322 Salt bridges: A:R.55, A:R.322, A:R.322 CIT.9: 11 residues within 4Å: Chain B: V.135, S.136, T.137, N.172, H.222, W.257, D.279, R.282, R.311, F.314 Ligands: CO.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.135 Hydrogen bonds: B:N.172, B:D.279, B:R.282 Water bridges: B:R.311 Salt bridges: B:H.222, B:R.282, B:R.311 CIT.10: 8 residues within 4Å: Chain B: S.22, R.55, Y.97, S.106, G.107, S.108, L.318, R.322 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.97 Hydrogen bonds: B:S.106, B:S.106, B:S.106, B:S.108, B:R.322 Water bridges: B:S.22, B:V.23, B:R.24, B:R.55, B:R.319, B:R.322, B:R.322, B:R.322 Salt bridges: B:R.55, B:R.322, B:R.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mohapatra, S.B. et al., Structure of an alpha-glucuronidase in complex with Co2+and citrate provides insights into the mechanism and substrate recognition in the family 4 glycosyl hydrolases. Biochem.Biophys.Res.Commun. (2019)

Release Date

2020-04-29

Peptides

Alpha-glucosidase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alpha-glucosidase, putative

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