SMTL ID : 4wmk.1

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

hetero-1-1-mer

Ligands

1 x BGC- XYS- XYS: alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose(Non-covalent)

BGC-XYS-XYS.1: 19 residues within 4Å: Chain A: D.139, E.169, Q.171, V.173, N.202, S.203, G.204, L.241, Q.244, C.270, W.272, W.273, H.296, N.298, C.299 Chain B: E.10, S.11 Ligands: MN.2, UDP.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.11, A:N.202, A:N.298

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

MN.2: 5 residues within 4Å: Chain A: D.139, D.141, H.296 Ligands: BGC-XYS-XYS.1, UDP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.139, A:D.141, A:D.141, A:H.296

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

UDP.3: 14 residues within 4Å: Chain A: M.17, F.18, T.19, L.27, K.30, D.139, L.140, D.141, H.296, N.298, C.299 Ligands: BGC-XYS-XYS.1, BGC-XYS-XYS.1, MN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:M.17, A:T.19, A:T.19, A:T.19, A:L.140, A:D.141, A:C.299 Water bridges: A:M.17, A:K.30, A:N.300 Salt bridges: A:K.30, A:H.296

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

SO4.4: 3 residues within 4Å: Chain A: R.168, D.262, C.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.263 Salt bridges: A:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Nat.Chem.Biol. (2015)

Release Date

2015-09-30

Peptides

Xyloside xylosyltransferase 1: A
Coagulation factor IX: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Xyloside xylosyltransferase 1

Coagulation factor IX

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