SMTL ID : 7ctm.1

Crystal structure of Thermotoga maritima alpha-glucuronidase (TM0752) in complex with NADH and D-glucuronic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 31 residues within 4Å: Chain A: I.18, G.19, G.21, S.22, V.23, R.24, F.25, M.49, D.50, V.51, H.52, R.55, T.95, A.96, Y.97, P.98, Y.99, S.106, G.107, T.137, L.150, T.170, A.171, N.172, V.174, F.192, C.193, H.194, L.318, R.322 Ligands: BDP.2 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.25, A:F.25 Hydrogen bonds: A:G.21, A:G.21, A:S.22, A:V.23, A:R.24, A:V.51, A:H.52, A:R.55, A:R.55, A:Y.97, A:Y.99, A:Y.99, A:T.137, A:N.172, A:N.172, A:F.192 Water bridges: A:R.24, A:R.24, A:Y.99, A:G.107, A:G.107, A:G.107, A:H.194, A:H.194, A:H.194, A:R.322 Salt bridges: A:R.24, A:R.322, A:R.322 NAI.4: 31 residues within 4Å: Chain B: I.18, G.19, G.21, S.22, V.23, R.24, F.25, M.49, D.50, V.51, H.52, R.55, T.95, A.96, Y.97, P.98, Y.99, S.106, G.107, T.137, L.150, T.170, A.171, N.172, V.174, F.192, C.193, H.194, L.318, R.322 Ligands: BDP.5 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:F.25, B:F.25 Hydrogen bonds: B:G.21, B:G.21, B:S.22, B:V.23, B:R.24, B:V.51, B:H.52, B:R.55, B:R.55, B:Y.97, B:Y.99, B:Y.99, B:T.137, B:N.172, B:N.172, B:F.192 Water bridges: B:R.24, B:R.24, B:Y.99, B:G.107, B:G.107, B:G.107, B:H.194, B:H.194, B:H.194, B:R.322 Salt bridges: B:R.24, B:R.322, B:R.322

2 x BDP: beta-D-glucopyranuronic acid(Non-covalent)

BDP.2: 14 residues within 4Å: Chain A: R.24, V.135, S.136, T.137, Y.138, N.172, C.193, H.222, W.257, D.279, R.282, R.311, F.314 Ligands: NAI.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.137, A:N.172, A:H.222, A:D.279 Water bridges: A:R.24, A:R.311, A:R.311 Salt bridges: A:R.24, A:R.282, A:R.282, A:R.311 BDP.5: 14 residues within 4Å: Chain B: R.24, V.135, S.136, T.137, Y.138, N.172, C.193, H.222, W.257, D.279, R.282, R.311, F.314 Ligands: NAI.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.137, B:N.172, B:H.222, B:D.279 Water bridges: B:R.24, B:R.311, B:R.311 Salt bridges: B:R.24, B:R.282, B:R.282, B:R.311

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

IPA.3: 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 A, 1 interactions with chain B Water bridges: A:T.453 Hydrophobic interactions: B:W.286 IPA.6: 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 B, 1 interactions with chain A Water bridges: B:T.453 Hydrophobic interactions: A:W.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mohapatra, S.B. et al., Structural basis of catalysis and substrate recognition by the NAD(H)-dependent alpha-d-glucuronidase from the glycoside hydrolase family 4. Biochem.J. (2021)

Release Date

2021-09-01

Peptides

Alpha-glucosidase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alpha-glucosidase, putative

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