SMTL ID : 6t2b.2 (1 other biounit)

Glycoside hydrolase family 109 from Akkermansia muciniphila in complex with GalNAc and NAD+.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.1: 12 residues within 4Å: Chain A: V.173, Y.201, H.203, L.205, E.215, R.219, Y.231, H.234, Y.314, R.316, H.379 Ligands: NAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.173 Hydrogen bonds: A:Y.201, A:R.219, A:R.219, A:Y.231, A:H.234, A:Y.314, A:H.379 Salt bridges: A:H.203, A:H.379 A2G.3: 11 residues within 4Å: Chain B: N.172, V.173, Y.201, H.203, E.215, R.219, Y.231, H.234, Y.314, H.379 Ligands: NAD.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.173 Hydrogen bonds: B:Y.201, B:R.219, B:R.219, B:Y.231, B:Y.231, B:H.234, B:H.379 Water bridges: B:Q.208 Salt bridges: B:H.203, B:H.379

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

NAD.2: 27 residues within 4Å: Chain A: I.48, G.49, G.51, G.52, R.53, C.73, D.74, L.75, L.79, D.102, S.120, T.121, D.122, W.123, H.126, R.128, I.129, E.143, V.144, N.172, G.214, E.215, W.218, Y.231, H.234, H.379 Ligands: A2G.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.53 Hydrogen bonds: A:G.51, A:G.52, A:R.53, A:R.53, A:L.75, A:D.102, A:W.123, A:H.126, A:R.128, A:N.172, A:N.172, A:Y.231 Water bridges: A:G.54, A:E.104, A:S.125, A:S.125, A:S.125 NAD.4: 28 residues within 4Å: Chain B: I.48, G.49, G.51, G.52, R.53, C.73, D.74, L.75, L.79, D.102, S.120, T.121, D.122, W.123, S.125, H.126, R.128, I.129, E.143, V.144, N.172, G.214, E.215, W.218, Y.231, H.234, H.379 Ligands: A2G.3 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.53 Hydrogen bonds: B:G.51, B:G.52, B:R.53, B:R.53, B:L.75, B:D.102, B:D.122, B:W.123, B:S.125, B:H.126, B:R.128, B:N.172, B:N.172, B:E.215 Water bridges: B:G.54, B:K.76, B:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teze, D. et al., The Catalytic Acid-Base in GH109 Resides in a Conserved GGHGG Loop and Allows for Comparable alpha-Retaining and beta-Inverting Activity in an N-Acetylgalactosaminidase from Akkermansia muciniphila. Acs Catalysis (2020)

Release Date

2020-02-26

Peptides

Glycosyl hydrolase family 109 protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Glycosyl hydrolase family 109 protein 2

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