6EJE: Human Xylosyltransferase 1

Name: PDB 6EJE: Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT
Published: 2018-05-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human Xylosyltransferase 1 in complex with peptide PAAEGSGEQDFT. Determined by X-ray diffraction at 2.43 Å resolution. Released 2 May 2018.

Method: X-ray diffraction
Resolution: 2.43 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,680
Mol. weight: 87.45 kDa
Ligands: PO4
Released: 2 May 2018

Explore 6EJE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EJE contains 34 α-helices and 37 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 34 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	262-270	9
α-helix	274-288	15
β-strand	296	1	1
β-strand	328-334	7	2
α-helix	339-349	11
β-strand	355-360	6	2
α-helix	365-377	13
β-strand	381-383	3	2
α-helix	396-410	15
β-strand	418-422	5	2
β-strand	426-428	3	3
α-helix	432-441	10
β-strand	446-447	2	2
β-strand	450	1	4
α-helix	455-462	8
β-strand	466-471	6	5
β-strand	474-480	7	5
α-helix	482-484	3
β-strand	485	1	1
β-strand	492	1	4
β-strand	497-499	3	2
α-helix	500-508	9
α-helix	512-520	9
α-helix	521-523	3
α-helix	527-529	3
α-helix	531-538	8
α-helix	542-544	3
β-strand	545-546	2	2
β-strand	551-553	3	3
α-helix	557-560	4
β-strand	569	1	5
β-strand	572-573	2	6
α-helix	576-579	4
α-helix	581-588	8
β-strand	596-598	3	3
α-helix	607-617	11
α-helix	619-621	3
β-strand	629-636	8	7
α-helix	637-639	3
α-helix	641-643	3
α-helix	646-666	21
β-strand	677-691	15	7
β-strand	695-706	12	7
β-strand	711-721	11	7
α-helix	722-723	2
β-strand	726	1	8
β-strand	737-743	7	9
β-strand	746-747	2	10
β-strand	752-753	2	10
β-strand	767-772	6	9
β-strand	778-785	8	8
β-strand	791-799	9	8
β-strand	805-808	4	9
α-helix	816-818	3
β-strand	819-827	9	8
β-strand	830-839	10	8
α-helix	840-842	3
β-strand	844-845	2	11
β-strand	848-849	2	11
α-helix	850-851	2
α-helix	852-858	7
α-helix	873-875	3
α-helix	885-896	12
α-helix	899-913	15
β-strand	914-921	8	7
α-helix	930	1
β-strand	931-932	2	7
α-helix	933-935	3
α-helix	945-947	3
α-helix	951-953	3

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	210-211	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Xylosyltransferase 1	A	protein	751	Homo sapiens	Q86Y38 (AlphaFold model)
Syndecan-1	B	protein	12	Homo sapiens	P18827 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6EJE_1 Xylosyltransferase 1 (chains A)
APLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISAL
SRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRI
AFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRM
ATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFL
KSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTF
STDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHI
VDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLR
SYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHL
YFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDA
KERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHY
KPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYM
EQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACP
VMQTCSQTAWSSFSPDPKSELGAVKPDGRLR

Sequence of entity 2 (B), FASTA

>6EJE_2 Syndecan-1 (chains B)
PAAEGSGEQDFT

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1. Briggs, D.C., Hohenester, E. Structure (2018) 26:801-809.e3. DOI 10.1016/j.str.2018.03.014 · PubMed

Other PDB entries of the same protein (UniProt Q86Y38 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FOA 1.87 Å, Human Xylosyltransferase 1 apo structure
6EJA 1.94 Å, Human Xylosyltransferase 1 in complex with peptide QEEEYSGGGQGG
6EJ7 2.0 Å, Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG
6EJ9 2.02 Å, Human Xylosyltransferase 1 in complex with peptide QEPEGSGGGQGG
6EJC 2.06 Å, Human Xylosyltransferase 1 in complex with peptide QEEEGSGVGQGG
6EJ8 2.09 Å, Human Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG
6EJB 2.56 Å, Human Xylosyltransferase 1 in complex with peptide QEEEGSAGGQGG
6EJD 2.68 Å, Human Xylosyltransferase 1 in complex with peptide QEEEGSGGPQGG

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