SMTL ID : 8qc5.1

crystal structure of NAD-dependent glycoside hydrolase from Arthrobacter sp. U41 in complex with NAD+ cofactor and citrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: G.31, G.33, H.34, M.35, D.56, P.57, Q.58, S.61, A.94, S.95, P.96, N.97, T.99, H.100, I.103, E.119, K.120, P.121, A.146, E.148, K.185, V.186, W.189, E.202, H.206, H.334 Ligands: CIT.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.120 Hydrogen bonds: A:H.34, A:M.35, A:S.61, A:S.95, A:K.120, A:E.148, A:V.186, A:E.202 Water bridges: A:G.33, A:A.36, A:H.79 Salt bridges: A:K.185, A:K.185 NAD.3: 28 residues within 4Å: Chain B: G.31, A.32, G.33, H.34, M.35, D.56, P.57, Q.58, S.61, A.94, S.95, P.96, N.97, T.99, H.100, I.103, E.119, K.120, P.121, A.146, E.148, K.185, V.186, W.189, E.202, H.206, H.334 Ligands: CIT.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.32, B:A.32, B:H.34, B:M.35, B:S.61, B:S.61, B:S.95, B:E.119, B:K.120, B:V.186, B:E.202 Water bridges: B:G.33, B:A.36, B:H.79, B:H.79 Salt bridges: B:K.185, B:K.185 pi-Cation interactions: B:K.120

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

CIT.2: 10 residues within 4Å: Chain A: H.34, R.179, F.180, F.182, L.183, K.185, H.296, A.333, H.334 Ligands: NAD.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.180, A:L.183 Hydrogen bonds: A:H.34, A:L.183 Water bridges: A:Y.149, A:N.190, A:N.190 Salt bridges: A:H.34, A:R.179, A:R.179, A:K.185, A:K.203, A:H.296, A:H.334, A:H.334 CIT.4: 10 residues within 4Å: Chain B: H.34, R.179, F.180, F.182, L.183, K.185, H.296, A.333, H.334 Ligands: NAD.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.180, B:L.183 Hydrogen bonds: B:H.34, B:L.183, B:K.185 Water bridges: B:R.179, B:N.190 Salt bridges: B:H.34, B:R.179, B:R.179, B:K.185, B:K.203, B:H.296, B:H.334, B:H.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaur, A. et al., Widespread Family of NAD + -Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism. J.Am.Chem.Soc. (2023)

Release Date

2023-12-27

Peptides

Oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Oxidoreductase

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