SMTL ID : 6gx2.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.07 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.155, D.157 Ligands: UDP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:D.157, A:D.157, H2O.9 MN.10: 3 residues within 4Å: Chain B: D.155, D.157 Ligands: UDP.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:D.157, B:D.157, H2O.25

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

UDP.2: 16 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, K.290, H.292, R.296 Ligands: MN.1, GOL.4 20 PLIP interactions: 20 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:V.156, A:D.157 Water bridges: A:K.68, A:S.129, A:R.132, A:R.296, A:R.296 Salt bridges: A:K.290, A:K.290, A:H.292, A:R.296, A:R.296 pi-Stacking: A:Y.70 UDP.11: 16 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, K.290, H.292, R.296 Ligands: MN.10, GOL.13 19 PLIP interactions: 19 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 Water bridges: B:K.68, B:S.129, B:R.132, B:R.296, B:R.296 Salt bridges: B:K.290, B:K.290, B:H.292, B:R.296, B:R.296 pi-Stacking: B:Y.70

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: H.177, F.180, T.189, Y.208, W.244, E.247 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.189, A:E.247 Water bridges: A:H.177 GOL.4: 9 residues within 4Å: Chain A: R.132, D.155, G.211, A.212, W.244, D.246, E.247 Ligands: UDP.2, GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.132, A:D.155, A:E.247, A:E.247 Water bridges: A:S.129, A:S.129, A:S.129 GOL.12: 7 residues within 4Å: Chain B: H.177, F.180, T.189, Y.208, W.244, E.247 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.189, B:T.189, B:E.247 Water bridges: B:H.177 GOL.13: 9 residues within 4Å: Chain B: R.132, D.155, G.211, A.212, W.244, D.246, E.247 Ligands: UDP.11, GOL.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.132, B:D.155, B:E.247, B:E.247 Water bridges: B:S.129, B:S.129, B:S.129

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

EDO.5: 8 residues within 4Å: Chain A: M.13, Y.15 Chain B: R.185, E.204, G.205, D.206, L.255, R.256 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.185, B:E.204, B:G.205, B:G.205, B:R.256, A:M.13 Water bridges: B:K.258 EDO.6: 5 residues within 4Å: Chain A: Y.15, P.16, N.45, I.48 Chain B: P.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.16, A:N.45 Water bridges: A:G.42 EDO.7: 4 residues within 4Å: Chain A: R.185 Chain B: V.14, Y.15, P.16 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.17, A:R.185 Hydrogen bonds: A:R.185 EDO.14: 8 residues within 4Å: Chain A: R.185, E.204, G.205, D.206, L.255, R.256 Chain B: M.13, Y.15 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.185, A:G.205, A:G.205, A:R.256, B:M.13 Water bridges: A:K.258 EDO.15: 5 residues within 4Å: Chain A: P.33 Chain B: Y.15, P.16, N.45, I.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.16, B:N.45 Water bridges: B:G.42 EDO.16: 4 residues within 4Å: Chain A: V.14, Y.15, P.16 Chain B: R.185 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:Q.17, B:R.185 Hydrogen bonds: B:R.185

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

SO4.8: 2 residues within 4Å: Chain A: T.110, G.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.111 Water bridges: A:T.110, A:R.112, A:R.112 SO4.9: 3 residues within 4Å: Chain A: R.120, Y.122, K.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.123 Water bridges: A:R.124 Salt bridges: A:R.120 SO4.17: 2 residues within 4Å: Chain B: T.110, G.111 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.110, B:G.111 Water bridges: B:T.110, B:R.112, B:R.112 SO4.18: 3 residues within 4Å: Chain B: R.120, Y.122, K.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.123 Water bridges: B:R.124 Salt bridges: B:R.120

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 glycerol. 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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