SMTL ID : 5m79.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.155, D.157, K.290 Ligands: U5P.2 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.155, A:D.157, H2O.1, H2O.2, U5P.2 MN.8: 4 residues within 4Å: Chain B: D.155, D.157, K.290 Ligands: U5P.9 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.155, B:D.157, U5P.9, H2O.14, H2O.15

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.2: 17 residues within 4Å: Chain A: V.64, F.65, A.66, I.67, K.68, Y.70, W.125, V.128, S.129, R.132, D.155, V.156, D.157, K.290, H.292, R.296 Ligands: MN.1 15 PLIP interactions: 15 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:R.296 Salt bridges: A:K.290, A:R.296 pi-Stacking: A:Y.70 U5P.9: 17 residues within 4Å: Chain B: V.64, F.65, A.66, I.67, K.68, Y.70, W.125, V.128, S.129, R.132, D.155, V.156, D.157, K.290, H.292, R.296 Ligands: MN.8 15 PLIP interactions: 15 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:Y.70, B:V.156, B:D.157 Water bridges: B:K.68, B:R.132, B:R.296 Salt bridges: B:K.290, B:R.296 pi-Stacking: B:Y.70

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: W.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.276 Water bridges: A:W.276 GOL.4: 7 residues within 4Å: Chain A: H.177, F.180, T.189, Y.208, W.244, E.247 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.177, A:T.189, A:E.247 GOL.5: 10 residues within 4Å: Chain A: M.158, H.177, P.178, A.212, E.247, L.268, W.269, D.270, A.287 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.177, A:A.287 Water bridges: A:E.247, A:D.270 GOL.10: 1 residues within 4Å: Chain B: W.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.276 Water bridges: B:W.276 GOL.11: 7 residues within 4Å: Chain B: H.177, F.180, T.189, Y.208, W.244, E.247 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.177, B:T.189, B:E.247 GOL.12: 10 residues within 4Å: Chain B: M.158, H.177, P.178, A.212, E.247, L.268, W.269, D.270, A.287 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.177, B:A.287 Water bridges: B:E.247

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

SO4.6: 3 residues within 4Å: Chain A: T.110, G.111, R.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.110, A:T.110, A:G.111 SO4.7: 5 residues within 4Å: Chain A: R.120, A.121, Y.122, K.123, R.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.123 Water bridges: A:R.124 Salt bridges: A:R.120 SO4.13: 3 residues within 4Å: Chain B: T.110, G.111, R.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.110, B:T.110, B:G.111 SO4.14: 5 residues within 4Å: Chain B: R.120, A.121, Y.122, K.123, R.124 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 UMP 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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