SMTL ID : 8pvs.1 (1 other biounit)

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 1.68 Å

Oligo State

monomer

Ligands

1 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.1: 11 residues within 4Å: Chain A: N.213, R.372, M.398, D.430, H.433, D.453, N.457, R.562, L.565, W.596, E.598 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.213, A:N.213, A:R.372, A:R.372, A:D.430, A:D.453, A:N.457, A:R.562, A:R.562 Water bridges: A:R.560 Salt bridges: A:R.562

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: V.6, K.7, V.8, L.25, D.26, T.43, G.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.8

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: H.48, N.130, S.131, Y.132, D.133, H.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.130, A:Y.132, A:D.133 FMT.4: 5 residues within 4Å: Chain A: R.85, M.123, D.125, N.206, I.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.85, A:R.85 FMT.5: 3 residues within 4Å: Chain A: R.194, I.196, G.238 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: S.81, R.126, D.128, N.129, D.133 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.81, A:R.126, A:D.128, A:D.133, H2O.11 CA.7: 3 residues within 4Å: Chain A: N.499, S.533, D.538 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.533, A:D.538, H2O.15, H2O.16, H2O.17

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

NA.8: 1 residues within 4Å: Chain A: T.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.20, A:T.20 NA.9: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.637 NA.10: 1 residues within 4Å: Chain A: V.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.155 Water bridges: A:N.157

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

Alpha-1,3-galactosidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-1,3-galactosidase B

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