SMTL ID : 8pxt.1

Targeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-trimer

Ligands

7 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.1: 12 residues within 4Å: Chain A: R.159, W.217, H.259, D.320, W.371, W.400, Y.426, D.428, Y.429, W.465, E.467 Ligands: NGA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.320, A:W.371, A:W.400 Hydrogen bonds: A:R.159, A:R.159, A:D.320, A:Y.426, A:D.428, A:E.467 Water bridges: A:D.188, A:H.259, A:E.467 NGA.2: 6 residues within 4Å: Chain A: R.323, W.400, K.401, H.422, Y.429 Ligands: NGA.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.400 Hydrogen bonds: A:R.323, A:R.323 NGA.3: 11 residues within 4Å: Chain A: Y.572, G.575, A.576, H.577, A.578, R.601, G.603, A.604, H.605, A.633, G.634 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.572 Hydrogen bonds: A:A.576, A:A.578, A:A.604, A:A.633, A:A.633 Water bridges: A:R.601 Salt bridges: A:R.601 NGA.6: 15 residues within 4Å: Chain A: E.550, E.582, N.629, K.631 Chain B: Y.572, G.575, A.576, H.577, A.578, R.601, G.603, A.604, H.605, A.633, G.634 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.572 Hydrogen bonds: B:A.576, B:A.578, B:R.601, B:R.601, B:A.604 Salt bridges: B:R.601 NGA.7: 12 residues within 4Å: Chain B: R.159, D.188, W.217, H.259, D.320, W.371, W.400, Y.426, D.428, Y.429, W.465, E.467 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:D.320 Hydrogen bonds: B:R.159, B:R.159, B:D.320, B:Y.426, B:D.428, B:E.467 Water bridges: B:H.259, B:R.323, B:Y.429, B:E.467 NGA.8: 13 residues within 4Å: Chain B: R.549, E.550, E.551 Chain C: Y.572, G.575, A.576, H.577, A.578, R.601, G.603, A.604, A.633, G.634 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.572 Hydrogen bonds: C:A.576, C:A.578, C:R.601, C:A.604, C:A.633, C:A.633, B:E.551 NGA.9: 11 residues within 4Å: Chain C: R.159, W.217, H.259, D.320, W.371, W.400, Y.426, D.428, Y.429, W.465, E.467 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:D.320 Hydrogen bonds: C:R.159, C:R.159, C:D.320, C:Y.426, C:D.428, C:E.467 Water bridges: C:W.371, C:D.428, C:Y.429

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain A: E.450 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.450 Water bridges: A:E.450 NA.5: 8 residues within 4Å: Chain A: P.19, A.20, S.91, I.135, S.136, T.138, P.139, F.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.20, A:S.91 NA.10: 5 residues within 4Å: Chain C: Y.587, N.589, T.623, Y.624, T.625 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.589 NA.11: 5 residues within 4Å: Chain C: P.268, F.269, S.271, L.272, T.274 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.274

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 1 residues within 4Å: Chain C: R.210 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jensen, M. et al., Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood. To Be Published

Release Date

2024-02-28

Peptides

Beta-N-acetylhexosaminidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Beta-N-acetylhexosaminidase