SMTL ID : 5m7d.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 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: GDU.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.10 MN.9: 3 residues within 4Å: Chain B: D.155, D.157 Ligands: GDU.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:D.157, B:D.157, H2O.24

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

GDU.2: 21 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, G.211, A.212, W.244, H.245, D.246, E.247, K.290, R.296 Ligands: MN.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:V.128 Hydrogen bonds: A:F.65, A:I.67, A:I.67, A:Y.70, A:Y.70, A:R.132, A:R.132, A:D.155, A:V.156, A:D.157, A:D.157, A:H.245, A:D.246, A:E.247 Water bridges: A:F.65, A:A.212, A:E.247, A:R.296, A:R.296, A:R.296 Salt bridges: A:K.290, A:K.290, A:R.296, A:R.296 pi-Stacking: A:Y.70 GDU.10: 21 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, G.211, A.212, W.244, H.245, D.246, E.247, K.290, R.296 Ligands: MN.9 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.128 Hydrogen bonds: B:F.65, B:I.67, B:I.67, B:Y.70, B:R.132, B:R.132, B:D.155, B:V.156, B:D.157, B:D.157, B:W.244, B:H.245, B:D.246, B:E.247 Water bridges: B:F.65, B:A.212, B:E.247, B:R.296, B:R.296, B:R.296 Salt bridges: B:K.290, B:K.290, B:R.296, B:R.296 pi-Stacking: B:Y.70

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.177, F.180, T.189, Y.208, W.244, E.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.189, A:E.247 GOL.4: 4 residues within 4Å: Chain A: M.7, Q.52, F.53 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.52, A:L.169 GOL.5: 5 residues within 4Å: Chain A: N.50, R.54, V.87, G.88, H.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.87 Water bridges: A:N.50, A:N.50 GOL.6: 8 residues within 4Å: Chain A: W.34, L.35, A.36, K.258, P.259, T.260 Chain B: Q.52 Ligands: GOL.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.35, A:K.258, B:Q.52 Water bridges: A:K.258 GOL.11: 6 residues within 4Å: Chain B: H.177, F.180, T.189, Y.208, W.244, E.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.189, B:T.189, B:E.247 GOL.12: 4 residues within 4Å: Chain B: M.7, Q.52, F.53 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.52, B:L.169 GOL.13: 5 residues within 4Å: Chain B: N.50, R.54, V.87, G.88, H.89 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.87 Water bridges: B:N.50, B:N.50 GOL.14: 8 residues within 4Å: Chain A: Q.52 Chain B: W.34, L.35, A.36, K.258, P.259, T.260 Ligands: GOL.4 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.35, B:K.258, A:Q.52 Water bridges: B:K.258

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

SO4.7: 2 residues within 4Å: Chain A: T.110, G.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.110, A:G.111 SO4.8: 3 residues within 4Å: Chain A: R.120, Y.122, K.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.123 Water bridges: A:R.124 Salt bridges: A:R.120, A:K.123 SO4.15: 2 residues within 4Å: Chain B: T.110, G.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.110, B:T.110, B:G.111 SO4.16: 3 residues within 4Å: Chain B: R.120, Y.122, K.123 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.123 Water bridges: B:R.124 Salt bridges: B:R.120, B:K.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2017-11-29

Peptides

Histo-blood group ABO system transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histo-blood group ABO system transferase

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