6XDS: PDB entry 6XDS

Crystal structure of MBP-TREM2 Ig domain fusion with fragment, 2-((4-bromophenyl)amino)ethan-1-ol. Determined by X-ray diffraction at 1.47 Å resolution. Released 17 Feb 2021.

Method: X-ray diffraction
Resolution: 1.47 Å
Organisms: Methanosarcina mazei, Homo sapiens
Chains: 1
Atoms: 4,464
Mol. weight: 55.13 kDa
Ligands: V5S
Released: 17 Feb 2021

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

Secondary structure: helices and β-sheets

6XDS contains 26 α-helices and 33 β-strands across 1 chain. 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: 26 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
α-helix	17-31	15
β-strand	35-38	4	1
α-helix	43-50	8
β-strand	59-63	5	1
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	2
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	3
α-helix	91-96	6
β-strand	98-99	2	4
β-strand	102-103	2	4
β-strand	106-111	6	1
β-strand	114-118	5	5
β-strand	128	1	6
α-helix	132-140	9
β-strand	145-147	3	5
α-helix	154-163	10
β-strand	167-172	6	7
β-strand	175-182	8	7
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	5
α-helix	229-231	3
α-helix	232-238	7
β-strand	242-245	4	5
α-helix	246-248	3
β-strand	249	1	6
β-strand	250	1	8
β-strand	253	1	8
α-helix	257	1
β-strand	258-259	2	9
β-strand	260-266	7	1
β-strand	267	1	2
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	1
β-strand	304	1	3
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	9
α-helix	330-331	2
α-helix	336-352	17
α-helix	357-367	11
β-strand	371-377	7	10
β-strand	382-387	6	11
β-strand	398-403	6	10
β-strand	410-415	6	10
β-strand	424-427	4	11
β-strand	430-437	8	11
β-strand	442-448	7	11
α-helix	452-454	3
β-strand	456-464	9	10
β-strand	467-479	13	10
α-helix	480-481	2
α-helix	482-485	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sugar ABC transporter substrate-binding protein,Triggering receptor expressed on myeloid cells 2	A	protein	492	Methanosarcina mazei, Homo sapiens	P0AEX9 (AlphaFold model), Q9NZC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XDS_1 Sugar ABC transporter substrate-binding protein,Triggering receptor expressed on myeloid cells 2 (chains A)
KTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDII
FWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKD
VGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEHAFNHGETAMTINGPWAWSNIDTSAV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLG
AVALKSYEEELVKDPRVAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAA
LAAAQTNAHDTTVFQGVAGQSLQVSCPYDSMKHWGRRKAWCRQLGEKGPCQRVVSTHNLW
LLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQCQSLHGSEADTLRKVLVEVLA
DPLDHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
V5S	2-[(4-bromophenyl)amino]ethan-1-ol	C8 H10 Br N O	1

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

Primary citation

Development of a robust crystallization platform for immune receptor TREM2 using a crystallization chaperone strategy. Byrne, N.J., Lee, A.C., Kostas, J. et al. Protein Expr Purif (2021) 179:105796-105796. DOI 10.1016/j.pep.2020.105796 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan
3O3U 1.5 Å, Crystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE)

Browse structure collections

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