SMTL ID : 5m7c.1

Blood group synthase AAGlyB in complex with UDP 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.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.5 MN.6: 3 residues within 4Å: Chain B: D.155, D.157 Ligands: UDP.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:D.157, B:D.157, H2O.11

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

UDP.2: 13 residues within 4Å: Chain A: F.65, A.66, I.67, K.68, Y.70, V.128, R.132, D.155, V.156, D.157, K.290, H.292 Ligands: MN.1 16 PLIP interactions: 16 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, A:D.157 Water bridges: A:K.68, A:R.132 Salt bridges: A:K.290, A:K.290, A:H.292 pi-Stacking: A:Y.70 UDP.7: 15 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.6 16 PLIP interactions: 16 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:R.132 Salt bridges: B:K.290, B:K.290, B:R.296, B:R.296 pi-Stacking: B:Y.70

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

PEG.3: 4 residues within 4Å: Chain A: I.46, K.83, V.87, H.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.83, A:H.163 Water bridges: A:D.47, A:D.47 PEG.4: 4 residues within 4Å: Chain A: V.14, Y.15, P.16 Chain B: R.185 No protein-ligand interaction detected (PLIP)

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

SO4.5: 2 residues within 4Å: Chain A: S.115, V.116 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.116 Water bridges: A:L.114, A:S.115 SO4.8: 2 residues within 4Å: Chain B: T.110, G.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.110, B:G.111, B:R.112

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 PEG 3350. 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
B

Histo-blood group ABO system transferase

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