SMTL ID : 5m7b.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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.7: 3 residues within 4Å: Chain B: D.155, D.157 Ligands: UDP.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:D.157, B:D.157, H2O.21

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:R.132, A:K.290, 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.8: 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.7, GOL.10 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:R.132, B:K.290, 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: 6 residues within 4Å: Chain A: H.177, F.180, T.189, Y.208, W.244, E.247 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: S.129, R.132, D.155, G.211, A.212, W.244, D.246, E.247 Ligands: UDP.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.129, A:R.132, A:D.155, A:G.211, A:D.246, A:D.246, A:E.247 Water bridges: A:A.212, A:E.247 GOL.9: 6 residues within 4Å: Chain B: H.177, F.180, T.189, Y.208, W.244, E.247 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.10: 9 residues within 4Å: Chain B: S.129, R.132, D.155, G.211, A.212, W.244, D.246, E.247 Ligands: UDP.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.129, B:R.132, B:D.155, B:G.211, B:D.246, B:D.246, B:E.247 Water bridges: B:A.212, B:H.245, B:E.247

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

SO4.5: 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 SO4.6: 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 SO4.11: 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 SO4.12: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocha, J. et al., Blood group synthase AAGlyB in complex with UDP 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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