5WPZ: MNDA PYD with MBP tag

Crystal structure of MNDA PYD with MBP tag. Determined by X-ray diffraction at 2.0 Å resolution. Released 15 Feb 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 22,797
Mol. weight: 318.88 kDa
Released: 15 Feb 2017

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

Secondary structure: helices and β-sheets

5WPZ contains 198 α-helices and 141 β-strands across 6 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, 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	91-96	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	232-237	6
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
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	315-324	10
β-strand	328-329	2	9
α-helix	330-331	2
α-helix	336-352	17
α-helix	357-369	13
α-helix	372-381	10
α-helix	384-386	3
α-helix	389-398	10
α-helix	400-403	4
α-helix	407-412	6
α-helix	415-425	11
α-helix	429-439	11
α-helix	443-445	3
α-helix	446-459	14

Chain B: 33 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	7-10	4	10
α-helix	17-31	15
β-strand	35-38	4	10
α-helix	43-52	10
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	91-96	6
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	132-140	9
β-strand	145-147	3	14
α-helix	154-163	10
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	232-237	6
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	372-378	7
α-helix	379-383	5
α-helix	384-386	3
α-helix	389-399	11
α-helix	407-412	6
α-helix	415-425	11
α-helix	429-439	11
α-helix	443-445	3
α-helix	446-459	14

Chain C: 35 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	19
α-helix	17-31	15
β-strand	35-38	4	19
α-helix	43-52	10
β-strand	59-63	5	19
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	20
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	21
α-helix	91-96	6
β-strand	98-99	2	22
β-strand	102-103	2	22
β-strand	106-111	6	19
β-strand	114-118	5	23
β-strand	128	1	24
α-helix	129-131	3
α-helix	132-139	8
α-helix	140-142	3
β-strand	145-147	3	23
α-helix	154-163	10
β-strand	167-172	6	25
β-strand	175-182	8	25
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	23
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	23
α-helix	246-248	3
β-strand	249-250	2	24
β-strand	253-254	2	24
α-helix	257	1
β-strand	258-259	2	26
β-strand	260-266	7	19
β-strand	267	1	20
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	19
β-strand	304	1	21
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	26
α-helix	330-331	2
α-helix	336-352	17
α-helix	357-369	13
α-helix	372-381	10
α-helix	384-386	3
α-helix	389-398	10
α-helix	400-403	4
α-helix	407-412	6
α-helix	415-425	11
α-helix	429-438	10
α-helix	439-441	3
α-helix	443-445	3
α-helix	446-460	15

Chain D: 33 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	7-10	4	27
α-helix	17-31	15
β-strand	35-38	4	27
α-helix	43-52	10
β-strand	59-63	5	27
α-helix	67-72	6
β-strand	76	1	28
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	29
α-helix	91-96	6
β-strand	98-99	2	30
β-strand	102-103	2	30
β-strand	106-111	6	27
β-strand	114-118	5	31
β-strand	128	1	32
α-helix	129-131	3
α-helix	132-140	9
β-strand	145-147	3	31
α-helix	154-161	8
β-strand	167-172	6	33
β-strand	175-182	8	33
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	31
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	31
α-helix	246-248	3
β-strand	249	1	32
β-strand	250	1	34
β-strand	253	1	34
α-helix	257	1
β-strand	258-259	2	35
β-strand	260-266	7	27
β-strand	267	1	28
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	27
β-strand	304	1	29
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	35
α-helix	330-331	2
α-helix	335-352	18
α-helix	357-369	13
α-helix	374-381	8
α-helix	384-386	3
α-helix	389-398	10
α-helix	400-403	4
α-helix	407-412	6
α-helix	415-425	11
α-helix	429-439	11
α-helix	443-445	3
α-helix	446-456	11

Chain E: 32 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	7-10	4	36
α-helix	17-31	15
β-strand	35-38	4	36
α-helix	43-53	11
β-strand	59-63	5	36
α-helix	64-66	3
α-helix	67-73	7
β-strand	76	1	37
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	38
α-helix	91-96	6
β-strand	98-99	2	39
β-strand	102-103	2	39
β-strand	106-111	6	36
β-strand	114-118	5	40
β-strand	128	1	41
α-helix	132-140	9
β-strand	145-147	3	40
α-helix	154-161	8
β-strand	167-172	6	42
β-strand	175-182	8	42
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	40
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	40
α-helix	246-248	3
β-strand	249-250	2	41
β-strand	253-254	2	41
β-strand	258-259	2	43
β-strand	260-266	7	36
β-strand	267	1	37
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-296	10
β-strand	301-302	2	36
β-strand	304	1	38
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	43
α-helix	330-331	2
α-helix	336-352	17
α-helix	357-369	13
α-helix	372-378	7
α-helix	379-384	6
α-helix	389-398	10
α-helix	400-403	4
α-helix	407-412	6
α-helix	415-425	11
α-helix	430-439	10
α-helix	443-445	3
α-helix	446-462	17

Chain F: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	7-10	4	44
α-helix	17-31	15
α-helix	33-34	2
β-strand	35-38	4	44
α-helix	43-53	11
β-strand	59-63	5	44
α-helix	64-66	3
α-helix	67-72	6
β-strand	76	1	45
α-helix	77-79	3
α-helix	83-86	4
β-strand	89	1	46
α-helix	91-96	6
β-strand	98-99	2	47
β-strand	102-103	2	47
β-strand	106-111	6	44
β-strand	114-118	5	48
β-strand	128	1	49
α-helix	132-140	9
β-strand	145-147	3	48
α-helix	154-161	8
β-strand	167-172	6	50
β-strand	175-182	8	50
α-helix	186-200	15
α-helix	210-218	9
β-strand	222-227	6	48
α-helix	229-231	3
α-helix	232-237	6
β-strand	242-245	4	48
α-helix	246-248	3
β-strand	249-250	2	49
β-strand	253-254	2	49
β-strand	258-259	2	51
β-strand	260-266	7	44
β-strand	267	1	45
α-helix	273-279	7
α-helix	280-284	5
α-helix	287-294	8
β-strand	301-302	2	44
β-strand	304	1	46
α-helix	305-311	7
α-helix	315-326	12
β-strand	328-329	2	51
α-helix	330-331	2
α-helix	336-351	16
α-helix	357-369	13
α-helix	372-379	8
α-helix	380-384	5
α-helix	389-398	10
α-helix	409-412	4
α-helix	415-425	11
α-helix	430-437	8
α-helix	446-455	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mbp-hmnda-pyd	A, B, C, D, E, F	protein	477	Homo sapiens	P0AEX9 (AlphaFold model), P41218 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5WPZ_1 MBP-hMNDA-PYD (chains A, B, C, D, E, F)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSA
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDA
ALAAAQTNAARAAAEYKKILLLKGFELMDDYHFTSIKSLLAYDLGLTTKMQEEYNRIKIT
DLMEKKFQGVACLDKLIELAKDMPSLKNLVNNLRKEKSKVAKKIKTQEKLEHHHHHH

Primary citation

Design of an expression system to enhance MBP-mediated crystallization. Jin, T.C., Chuenchor, W., Jiang, J. et al. Sci Rep (2017) 7:40991-40991. DOI 10.1038/srep40991 · 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 5WPZ 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.