7KD4: PDB entry 7KD4

Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329 -388), fused to MBP. Space group P21. Determined by X-ray diffraction at 1.31 Å resolution. Released 15 Sept 2021.

Method: X-ray diffraction
Resolution: 1.31 Å
Organisms: Serratia sp. (strain FS14), Menangle virus
Chains: 2
Atoms: 8,463
Mol. weight: 96.49 kDa
Released: 15 Sept 2021

Explore 7KD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KD4 contains 60 α-helices and 48 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: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
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	91-94	4
α-helix	95-97	3
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	132-141	10
β-strand	145-147	3	5
α-helix	154-156	3
α-helix	158-163	6
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	336-351	16
α-helix	357-369	13
α-helix	1335-1352	18
α-helix	1356-1368	13
α-helix	1372-1384	13

Chain B: 30 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	7-10	4	10
α-helix	17-31	15
β-strand	35-38	4	10
α-helix	43-51	9
β-strand	59-63	5	10
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	11
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	12
α-helix	91-94	4
α-helix	95-97	3
β-strand	98-99	2	13
β-strand	102-103	2	13
β-strand	106-111	6	10
β-strand	114-118	5	14
β-strand	128	1	15
α-helix	129-131	3
α-helix	132-141	10
β-strand	145-147	3	14
α-helix	154-156	3
α-helix	158-163	6
β-strand	167-172	6	16
β-strand	175-182	8	16
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	14
α-helix	229-231	3
α-helix	232-238	7
β-strand	242-245	4	14
α-helix	246-248	3
β-strand	249	1	15
β-strand	250	1	17
β-strand	253	1	17
α-helix	257	1
β-strand	258-259	2	18
β-strand	260-266	7	10
β-strand	267	1	11
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	10
β-strand	304	1	12
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	18
α-helix	330-331	2
α-helix	336-352	17
α-helix	357-368	12
α-helix	1335-1352	18
α-helix	1356-1368	13
α-helix	1372-1384	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltodextrin-binding protein and Phosphoprotein fusion protein	A, B	protein	431	Serratia sp. (strain FS14), Menangle virus	P0AEX9 (AlphaFold model), Q91MK1

Sequence of entity 1 (A, B), FASTA

>7KD4_1 Maltodextrin-binding protein and Phosphoprotein fusion protein (chains A, B)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDA
ALAAAQTNAAAKSSAASPAALSGYKMTLLALIKESIPNQAKRQKFEMQVGGIRNEQDFKN
LRREIIRSAAQ

Primary citation

Structural Analysis of the Menangle Virus P Protein Reveals a Soft Boundary between Ordered and Disordered Regions. Webby, M.N., Herr, N., Bulloch, E.M.M. et al. Viruses (2021) 13. DOI 10.3390/v13091737 · 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)
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
3O3U 1.5 Å, Crystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE)

Browse structure collections

About this viewer

MolViewer shows 7KD4 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.