3PGF: Maltose-binding periplasmic protein

Crystal structure of maltose bound MBP with a conformationally specific synthetic antigen binder (sAB). Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Mar 2011.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 3
Atoms: 6,592
Mol. weight: 92.84 kDa
Released: 9 Mar 2011

Explore 3PGF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PGF contains 44 α-helices and 66 β-strands across 3 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, 23 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	91-97	7
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	178	1	7
β-strand	181	1	7
α-helix	185-200	16
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	249-250	2	6
β-strand	253-254	2	6
α-helix	257	1
β-strand	258-259	2	8
β-strand	260-266	7	1
β-strand	267	1	2
α-helix	273-278	6
α-helix	279-284	6
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	8
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-365	9

Chain H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-52	8	10
β-strand	57-59	3	10
β-strand	67-72	6	9
α-helix	73-75	3
β-strand	77-82	6	9
α-helix	84-86	3
β-strand	88-95	8	10
β-strand	102-103	2	10
β-strand	107-111	5	10
α-helix	114-116	3
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
α-helix	125-127	3
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	159	1	13
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-185	10	12
α-helix	186-188	3
β-strand	195-200	6	13
α-helix	201-203	3
β-strand	205-210	6	13
α-helix	213-215	3

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-25	7	14
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-90	7	15
α-helix	96	1
β-strand	97-98	2	15
β-strand	102-107	6	15
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-154	2	18
β-strand	159-163	5	17
α-helix	164-167	4
β-strand	173-182	10	17
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	205-210	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein	A	protein	398	Escherichia coli	P0AEX9 (AlphaFold model)
SAB Heavy Chain	H	protein	231	Homo sapiens	P0DOX5 (AlphaFold model)
SAB Light Chain	L	protein	215	Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3PGF_1 Maltose-binding periplasmic protein (chains A)
MKHHHHHHHHHHSSDYKDDDDKGENLYFQGSKIEEGKLVIWINGDKGYNGLAEVGKKFEK
DTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKL
YPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMF
NLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTD
YSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAA
SPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEI
MPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTN

Sequence of entity 2 (H), FASTA

>3PGF_2 SAB Heavy Chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSSSYIHWVRQAPGKGLEWVAYISSYSGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARTPWWYWSGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (L), FASTA

>3PGF_3 SAB Light Chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYIPVTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins. Rizk, S.S., Paduch, M., Heithaus, J.H. et al. Nat Struct Mol Biol (2011) 18:437-442. DOI 10.1038/nsmb.2002 · 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
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

Browse structure collections

About this viewer

MolViewer shows 3PGF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.