SMTL ID : 6bsv.1

Crystal structure of Xyloglucan Xylosyltransferase binary form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.112, D.114, H.262, V.264 Ligands: UDP.2, NO3.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.112, A:D.114, A:H.262 MN.5: 6 residues within 4Å: Chain B: D.112, D.114, H.262, V.264 Ligands: UDP.6, NO3.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.112, B:D.114, B:D.114, B:H.262

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

UDP.2: 15 residues within 4Å: Chain A: T.40, G.41, S.42, A.43, G.87, F.88, A.90, K.91, W.110, D.112, S.113, D.114, K.267 Ligands: MN.1, NO3.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.40, A:G.41, A:G.41, A:F.88, A:S.113, A:S.113 Salt bridges: A:K.267, A:K.267 UDP.6: 16 residues within 4Å: Chain B: T.40, G.41, S.42, A.43, G.87, F.88, A.90, K.91, W.110, D.112, S.113, D.114, G.265, K.267 Ligands: MN.5, NO3.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.41, B:G.41, B:S.42, B:F.88, B:D.112, B:S.113, B:D.114 Water bridges: B:G.265 Salt bridges: B:K.267, B:K.267

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 7 residues within 4Å: Chain A: Y.132, N.140, Y.144, V.222, Y.223, L.224, E.225 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.140, A:V.222, A:Y.223, A:L.224, A:L.224 TRS.7: 7 residues within 4Å: Chain B: Y.132, N.140, Y.144, V.222, Y.223, L.224, E.225 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.140, B:N.140, B:V.222, B:L.224, B:L.224

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.4: 8 residues within 4Å: Chain A: D.112, D.114, H.262, V.264, G.265, K.267 Ligands: MN.1, UDP.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.265, A:K.267 NO3.8: 8 residues within 4Å: Chain B: D.112, D.114, H.262, V.264, G.265, K.267 Ligands: MN.5, UDP.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.265, B:K.267 Water bridges: B:C.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Culbertson, A.T. et al., Structure of xyloglucan xylosyltransferase 1 reveals simple steric rules that define biological patterns of xyloglucan polymers. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-05-23

Peptides

Xyloglucan 6-xylosyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xyloglucan 6-xylosyltransferase 1

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