SMTL ID : 6gx0.1

Blood group synthase AAGlyB in complex with UDP-Gal and cryoprotected with PEG 3350

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 2 residues within 4Å: Chain A: D.157 Ligands: GDU.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.157, H2O.1, H2O.11 MN.10: 2 residues within 4Å: Chain B: D.157 Ligands: GDU.11 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.157, H2O.17, H2O.27

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

GDU.2: 19 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 Ligands: MN.1 25 PLIP interactions: 25 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:D.155, A:V.156, A:D.157, A:D.157, A:W.244, A:D.246, A:E.247 Water bridges: A:F.65, A:S.129, A:S.129, A:S.129, A:S.129, A:G.211, A:E.247, A:E.247 pi-Stacking: A:Y.70 GDU.11: 19 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 Ligands: MN.10 24 PLIP interactions: 24 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:S.129, B:S.129, B:S.129, B:S.129, B:G.211, B:E.247, B:E.247 pi-Stacking: B:Y.70

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

SO4.3: 2 residues within 4Å: Chain A: T.110, G.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.110, A:G.111 Water bridges: A:R.112, A:R.112 SO4.4: 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 SO4.5: 2 residues within 4Å: Chain A: K.252, R.256 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Water bridges: B:S.9, B:R.12, B:R.12, A:Y.199, A:K.252, A:K.252, A:K.252, A:K.252, A:K.252, A:R.256, A:R.256 Salt bridges: A:K.252, A:R.256 SO4.12: 2 residues within 4Å: Chain B: T.110, G.111 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.110, B:T.110, B:G.111 Water bridges: B:R.112, B:R.112 SO4.13: 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 SO4.14: 2 residues within 4Å: Chain B: K.252, R.256 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Water bridges: A:S.9, A:R.12, A:R.12, B:Y.199, B:K.252, B:K.252, B:K.252, B:K.252, B:K.252, B:R.256, B:R.256 Salt bridges: B:K.252, B:R.256

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

PEG.6: 5 residues within 4Å: Chain A: I.46, K.83, H.84, V.87, H.163 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.83 PEG.15: 5 residues within 4Å: Chain B: I.46, K.83, H.84, V.87, H.163 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.163 Water bridges: B:K.83

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

EDO.7: 3 residues within 4Å: Chain A: T.189, V.243, W.244 No protein-ligand interaction detected (PLIP) EDO.8: 7 residues within 4Å: Chain A: R.185, E.204, G.205, D.206, L.255 Chain B: M.13, Y.15 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.185, A:G.205, A:G.205, B:M.13 Water bridges: A:L.255, A:K.258, A:K.258, B:P.11 EDO.9: 5 residues within 4Å: Chain A: C.24, R.25, K.26, D.27, R.281 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.26, A:D.27, A:R.281, A:R.281 Water bridges: A:C.24, A:R.25 EDO.16: 3 residues within 4Å: Chain B: T.189, V.243, W.244 No protein-ligand interaction detected (PLIP) EDO.17: 7 residues within 4Å: Chain A: M.13, Y.15 Chain B: R.185, E.204, G.205, D.206, L.255 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.185, B:G.205, B:G.205, A:M.13, A:Y.15 Water bridges: B:L.255, B:R.256, A:P.11, A:Y.15 EDO.18: 5 residues within 4Å: Chain B: C.24, R.25, K.26, D.27, R.281 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.26, B:D.27, B:R.281, B:R.281 Water bridges: B:C.24, B:R.25

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 PEG 3350. 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)

Related Entries With Identical Sequence