SMTL ID : 2ixb.1

Crystal structure of N-ACETYLGALACTOSAMINIDASE in complex with GalNAC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: A.27, G.29, L.30, R.31, A.51, D.52, P.53, D.54, M.57, N.80, S.98, S.99, P.100, W.101, W.103, H.104, H.107, E.121, V.122, N.150, S.208, E.209, W.212, Y.225, H.228 Ligands: A2G.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.31, A:R.31 Hydrogen bonds: A:L.30, A:R.31, A:R.31, A:D.54, A:N.80, A:S.99, A:W.101, A:N.150, A:N.150, A:Y.225 Water bridges: A:G.29, A:R.31, A:G.32 pi-Stacking: A:W.103 NAD.6: 26 residues within 4Å: Chain B: A.27, G.29, L.30, R.31, A.51, D.52, P.53, D.54, M.57, N.80, S.98, S.99, P.100, W.101, W.103, H.104, H.107, E.121, V.122, N.150, S.208, E.209, W.212, Y.225, H.228 Ligands: A2G.7 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:R.31, B:R.31 Hydrogen bonds: B:L.30, B:R.31, B:R.31, B:D.54, B:N.80, B:S.99, B:W.101, B:N.150, B:N.150, B:E.209 Water bridges: B:G.29, B:R.31, B:G.32 pi-Stacking: B:W.103

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

A2G.2: 12 residues within 4Å: Chain A: V.151, Y.179, H.181, L.183, V.186, E.209, R.213, Y.225, H.228, Y.307, M.375 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:Y.179, A:R.213, A:Y.225, A:H.228, A:Y.307 Water bridges: A:N.150 Salt bridges: A:H.181 A2G.7: 12 residues within 4Å: Chain B: V.151, Y.179, H.181, L.183, V.186, E.209, R.213, Y.225, H.228, Y.307, M.375 Ligands: NAD.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.151 Hydrogen bonds: B:R.213, B:Y.225, B:Y.225, B:H.228 Water bridges: B:N.150 Salt bridges: B:H.181

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 7 residues within 4Å: Chain A: C.386, E.391, A.392, P.394, T.437, I.440, Y.444 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.394, A:T.437, A:I.440, A:Y.444, A:Y.444 Hydrogen bonds: A:T.437 MRD.4: 3 residues within 4Å: Chain A: K.350, W.351, Y.355 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.351 Hydrogen bonds: A:K.350 MRD.8: 7 residues within 4Å: Chain B: C.386, E.391, A.392, P.394, T.437, I.440, Y.444 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.394, B:T.437, B:I.440, B:Y.444, B:Y.444 Hydrogen bonds: B:T.437, B:Y.444 MRD.9: 3 residues within 4Å: Chain B: K.350, W.351, Y.355 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.351 Hydrogen bonds: B:K.350, B:Y.355

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 6 residues within 4Å: Chain A: S.138, E.139, G.142, P.144, V.397, Y.398 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.139, A:V.397, A:Y.398 Hydrogen bonds: A:S.138 Water bridges: A:L.145 MPD.10: 6 residues within 4Å: Chain B: S.138, E.139, G.142, P.144, V.397, Y.398 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.139, B:V.397, B:Y.398 Hydrogen bonds: B:S.138 Water bridges: B:L.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Q.P. et al., Bacterial Glycosidases for the Production of Universal Red Blood Cells. Nat.Biotechnol. (2007)

Release Date

2007-04-10

Peptides

ALPHA-N-ACETYLGALACTOSAMINIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ALPHA-N-ACETYLGALACTOSAMINIDASE

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