5M13: Synthetic nanobody

Synthetic nanobody in complex with MBP. Determined by X-ray diffraction at 1.37 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 1.37 Å
Organisms: Escherichia coli, synthetic construct
Chains: 2
Atoms: 4,567
Mol. weight: 55.03 kDa
Released: 15 Nov 2017

Explore 5M13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M13 contains 28 α-helices and 35 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: 25 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	7-10	4	1
α-helix	17-31	15
β-strand	35-38	4	1
α-helix	43-51	9
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	91-95	5
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	129-131	3
α-helix	132-140	9
β-strand	145-147	3	5
α-helix	154-161	8
β-strand	167-171	5	7
β-strand	176-182	7	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	254-255	2
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	357-365	9

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	10-13	4	11
β-strand	18-26	9	10
β-strand	33-39	7	11
β-strand	46-52	7	11
β-strand	57-60	4	11
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	11
α-helix	109-111	3
β-strand	114-115	2	11
β-strand	119-124	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein	A	protein	373	Escherichia coli	P0AEX9 (AlphaFold model)
synthetic Nanobody L2_C06 (a-MBP#2)	B	protein	126	synthetic construct

Sequence of entity 1 (A), FASTA

>5M13_1 Maltose-binding periplasmic protein (chains A)
GPSKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGP
DIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIY
NKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYD
IKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDT
SKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDK
PLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTV
DEALKDAQTPGSA

Sequence of entity 2 (B), FASTA

>5M13_2 synthetic Nanobody L2_C06 (a-MBP#2) (chains B)
SQVQLVESGGGSVQAGGSLRLSCVASGDIKYISYLGWFRQAPGKEREGVAALYTSTGRTY
YADSVKGRFTVSLDNAKNTVYLQMNSLKPEDTALYYCAAAEWGSQSPLTQWFYRYWGQGT
QVTVSA

Primary citation

Synthetic single domain antibodies for the conformational trapping of membrane proteins. Zimmermann, I., Egloff, P., Hutter, C.A. et al. Elife (2018) 7. DOI 10.7554/eLife.34317 · 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…
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
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
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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