SMTL ID : 4wlz.3 (2 other biounits)

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese and UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.139, D.141, H.296 Ligands: UDP.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.139, A:D.141, A:D.141, A:H.296 MN.4: 5 residues within 4Å: Chain B: D.139, D.141, H.296, N.298 Ligands: UDP.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.139, B:D.141, B:D.141, B:H.296

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

UDP.2: 15 residues within 4Å: Chain A: M.17, F.18, T.19, L.27, D.139, L.140, D.141, H.296, N.298, C.299 Chain B: W.272, R.274, D.275, H.276 Ligands: MN.1 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:D.275, A:L.27 Hydrogen bonds: B:R.274, A:M.17, A:T.19, A:T.19, A:T.19, A:L.140, A:D.141, A:D.141, A:C.299 Salt bridges: B:H.276, B:H.276, A:K.30, A:H.296 UDP.5: 15 residues within 4Å: Chain A: W.272, D.275, H.276 Chain B: M.17, F.18, T.19, L.27, K.30, D.139, L.140, D.141, H.296, N.298, C.299 Ligands: MN.4 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:M.17, B:T.19, B:T.19, B:T.19, B:L.140, B:C.299 Salt bridges: B:K.30, A:H.276, A:H.276 Hydrophobic interactions: A:D.275

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

SO4.3: 5 residues within 4Å: Chain A: R.175, R.182, Y.278 Chain B: G.108, S.109 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.182, B:G.108, B:S.109 Salt bridges: A:R.175

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

2015-11-04

Peptides

Xyloside xylosyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xyloside xylosyltransferase 1

Related Entries With Identical Sequence