SMTL ID : 6gx1.1

Blood group synthase AAGlyB in complex with UDP-GalNAc and cryoprotected with PEG 3350

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: D.157 Ligands: UD2.2, UDP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.157, H2O.1, H2O.1 MN.8: 3 residues within 4Å: Chain B: D.157 Ligands: UD2.9, UDP.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.157, H2O.13, H2O.13

2 x UD2: URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE(Non-covalent)

UD2.2: 15 residues within 4Å: Chain A: F.65, A.66, I.67, K.68, Y.70, W.125, V.128, S.129, R.132, D.155, V.156, D.157, W.244 Ligands: MN.1, UDP.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.128, A:W.244 Hydrogen bonds: A:F.65, A:F.65, A:I.67, A:I.67, A:Y.70, A:Y.70, A:V.156, A:D.157, A:D.157 Water bridges: A:S.129, A:R.132 pi-Stacking: A:Y.70 UD2.9: 15 residues within 4Å: Chain B: F.65, A.66, I.67, K.68, Y.70, W.125, V.128, S.129, R.132, D.155, V.156, D.157, W.244 Ligands: MN.8, UDP.10 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.128, B:W.244 Hydrogen bonds: B:F.65, B:F.65, B:I.67, B:I.67, B:Y.70, B:Y.70, B:V.156, B:D.157, B:D.157 Water bridges: B:S.129, B:R.132 pi-Stacking: B:Y.70

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.3: 13 residues within 4Å: Chain A: F.65, A.66, I.67, K.68, Y.70, V.128, S.129, R.132, D.155, V.156, D.157 Ligands: MN.1, UD2.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.128 Hydrogen bonds: A:F.65, A:F.65, A:I.67, A:I.67, A:Y.70, A:Y.70, A:D.155, A:V.156, A:D.157, A:D.157 Water bridges: A:R.132 pi-Stacking: A:Y.70 UDP.10: 13 residues within 4Å: Chain B: F.65, A.66, I.67, K.68, Y.70, V.128, S.129, R.132, D.155, V.156, D.157 Ligands: MN.8, UD2.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.128 Hydrogen bonds: B:F.65, B:F.65, B:I.67, B:I.67, B:Y.70, B:V.156, B:D.157, B:D.157 Water bridges: B:R.132 pi-Stacking: B:Y.70

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: T.110, G.111 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.111 Water bridges: A:T.110, A:R.112, A:R.112, A:R.112, A:R.112 SO4.5: 4 residues within 4Å: Chain A: R.120, A.121, Y.122, K.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.121, A:K.123 Salt bridges: A:R.120 SO4.6: 2 residues within 4Å: Chain A: R.142, R.143 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.141, A:R.143, A:R.143 Salt bridges: A:R.142, A:R.143 SO4.11: 2 residues within 4Å: Chain B: T.110, G.111 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.110, B:G.111 Water bridges: B:T.110, B:R.112, B:R.112, B:R.112, B:R.112 SO4.12: 4 residues within 4Å: Chain B: R.120, A.121, Y.122, K.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.121, B:K.123 Salt bridges: B:R.120 SO4.13: 2 residues within 4Å: Chain B: R.142, R.143 5 PLIP interactions: 5 interactions with chain B Water bridges: B:E.141, B:R.143, B:R.143 Salt bridges: B:R.142, B:R.143

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: I.46, K.83, H.84, H.163 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.163 PEG.14: 4 residues within 4Å: Chain B: I.46, K.83, H.84, H.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.84, B:H.163 Water bridges: B:D.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocha, J. et al., Blood group synthase AAGlyB in complex with UDP-GalNAc and cryoprotected with PEG 3350. To be published

Release Date

2019-07-10

Peptides

ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)

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