SMTL ID : 6ej7.1

Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: N.569, L.590 No protein-ligand interaction detected (PLIP)

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

UDX.2: 26 residues within 4Å: Chain A: V.125, V.126, H.127, D.153, R.155, T.182, I.183, W.184, G.185, L.189, S.215, A.216, D.286, W.287, L.318, E.321, T.345, W.347, Y.357, C.366, S.367, P.368, R.390, K.391 Chain B: A.6 Ligands: PO4.7 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:V.125, A:H.127, A:D.153, A:D.153, A:R.155, A:T.182, A:W.184, A:D.286, A:W.287, A:Y.357, A:C.366, A:S.367 Water bridges: A:H.127, A:D.153, A:R.155, A:W.184, A:S.215, A:A.217, A:K.391, A:K.391 Salt bridges: A:R.390, A:R.390, A:R.390, A:K.391, A:K.391 pi-Stacking: A:H.127

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: S.167, Y.170, S.171, V.173, R.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.173, A:V.173

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 8 residues within 4Å: Chain A: R.454, A.455, S.458, D.710, I.711, V.721, M.722, Q.723 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.458, A:I.711, A:I.711, A:I.711 Salt bridges: A:R.454 PO4.5: 7 residues within 4Å: Chain A: G.128, R.129, R.155, S.156, Y.158 Ligands: PO4.7, PO4.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.155, A:R.155, A:S.156 Water bridges: A:R.129, A:Y.158 Salt bridges: A:R.129 PO4.6: 1 residues within 4Å: Chain A: R.174 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.174, A:R.174 Salt bridges: A:R.174 PO4.7: 7 residues within 4Å: Chain A: H.127, G.128, D.153, R.155, S.156 Ligands: UDX.2, PO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.128, A:S.156, A:S.156 Salt bridges: A:R.155 PO4.8: 5 residues within 4Å: Chain A: N.157, H.160, R.161, L.164, R.179 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.157, A:R.161 Water bridges: A:N.157, A:N.157, A:R.179 Salt bridges: A:H.160, A:R.179 PO4.9: 8 residues within 4Å: Chain A: R.129, R.155, S.156, N.157, Y.158, R.161, D.431 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.155, A:N.157, A:N.157, A:Y.158, A:D.431 Water bridges: A:R.129, A:R.129, A:R.129 Salt bridges: A:R.129 PO4.10: 9 residues within 4Å: Chain A: H.445, A.448, P.471, M.472, G.473, H.474, P.475, H.494, H.495 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.472, A:G.473, A:G.473 Water bridges: A:H.494, A:H.495 Salt bridges: A:H.445 PO4.11: 4 residues within 4Å: Chain A: Y.587, D.588, I.589, Y.600 No protein-ligand interaction detected (PLIP) PO4.12: 4 residues within 4Å: Chain A: E.296, Y.297, F.300, S.301 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.296, A:S.301

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

EDO.13: 9 residues within 4Å: Chain A: V.395, V.396, N.397, F.482, D.485, R.486, F.487, L.544, F.548 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.485 Water bridges: A:D.485 EDO.14: 8 residues within 4Å: Chain A: Q.45, P.46, P.47, I.51, L.60, R.69, Q.70, G.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.70, A:Q.70 EDO.15: 5 residues within 4Å: Chain A: A.187, L.261, E.262, S.314, Y.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.262, A:S.314 EDO.16: 8 residues within 4Å: Chain A: G.527, R.528, L.529, W.564, V.570, V.572, H.619, V.624 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.528 Water bridges: A:G.527

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

PEG.17: 9 residues within 4Å: Chain A: S.131, R.132, Q.135, Y.158, Q.162, D.736, S.739, E.740, L.741 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.132, A:Q.135, A:Q.162, A:S.739 Water bridges: A:E.740 PEG.18: 9 residues within 4Å: Chain A: P.579, R.609, P.610, G.611, A.683, N.686, W.697, S.700, L.701 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.686, A:W.697 Water bridges: A:A.683

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Briggs, D.C. et al., Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1. Structure (2018)

Release Date

2018-05-02

Peptides

Xylosyltransferase 1: A
Protein AMBP: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xylosyltransferase 1

Protein AMBP

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