4WVJ: PDB entry 4WVJ

Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with an inhibitor peptide (pep3). Determined by X-ray diffraction at 1.95 Å resolution. Released 23 Sept 2015.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Escherichia coli K-12, Staphylococcus aureus subsp. aureus str. Newman, Staphylococcus aureus
Chains: 2
Atoms: 4,468
Mol. weight: 60.69 kDa
Released: 23 Sept 2015

Explore 4WVJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WVJ contains 33 α-helices and 41 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: 32 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	1
α-helix	23-37	15
β-strand	42-44	3	1
α-helix	49-56	8
β-strand	65-69	5	1
α-helix	70-72	3
α-helix	73-78	6
β-strand	82	1	2
α-helix	83-85	3
α-helix	89-92	4
β-strand	95	1	3
α-helix	97-102	6
β-strand	104-105	2	4
β-strand	108-109	2	4
β-strand	112-117	6	1
β-strand	120-124	5	5
β-strand	134	1	6
α-helix	135-137	3
α-helix	138-146	9
β-strand	151-153	3	5
α-helix	160-169	10
β-strand	173-178	6	7
β-strand	181-188	8	7
α-helix	192-206	15
α-helix	216-224	9
β-strand	228-233	6	5
α-helix	235-237	3
α-helix	238-244	7
β-strand	248-251	4	5
α-helix	252-254	3
β-strand	255	1	6
β-strand	256	1	8
β-strand	259	1	8
α-helix	263	1
β-strand	264-265	2	9
β-strand	266-272	7	1
β-strand	273	1	2
α-helix	279-285	7
α-helix	286-290	5
α-helix	293-302	10
β-strand	307-308	2	1
β-strand	310	1	3
α-helix	311-317	7
α-helix	321-332	12
β-strand	334-335	2	9
α-helix	336-337	2
α-helix	342-358	17
α-helix	363-375	13
β-strand	378-385	8	10
β-strand	397-402	6	10
α-helix	403-404	2
β-strand	415-419	5	10
β-strand	425-432	8	10
β-strand	437	1	11
β-strand	438-441	4	12
β-strand	444-447	4	12
β-strand	450-452	3	12
α-helix	455-457	3
α-helix	458-462	5
β-strand	473-474	2	12
α-helix	475-477	3
β-strand	487	1	11
α-helix	488-489	2
β-strand	492-493	2	13
β-strand	494-496	3	10
β-strand	503	1	14
α-helix	506-509	4
α-helix	511	1
β-strand	512-513	2	13
α-helix	514-516	3
β-strand	517-522	6	10

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	204-207	4
β-strand	208-211	4	10
β-strand	213	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein,Signal peptidase IB	A	protein	533	Escherichia coli K-12, Staphylococcus aureus subsp. aureus str. Newman	P0AEY0 (AlphaFold model)
inhibitor peptide (PEP3)	D	protein	14	Staphylococcus aureus

Sequence of entity 1 (A), FASTA

>4WVJ_1 Maltose-binding periplasmic protein,Signal peptidase IB (chains A)
MSYYHHHHHHHMLVIWINGDKGYNGLAQVGKKFEKDTGIKVTVEHPYKLEEKFPQVAATG
DGPDIIFWAHDRFGGYACSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALS
LIYNKDLLPNPPKTWEEIPALDGELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENG
KYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSN
IDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVN
KDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGR
QTVDEALKDAQTNAGAIVTPYTIKGESMDPTLKDGERVAVNIVGYKTGGLEKGNVVVFHA
NKNDDYVKRVIGVPGDKVEYKNDTLYVNGKKQDEPYLNYNLKHKQGDYITGTFQVKDLPN
ANPKSNVIPKGKYLVLGDNREVSKDSRAFGLIDEDQIVGKVSFRFWSHPQFEK

Sequence of entity 2 (D), FASTA

>4WVJ_2 inhibitor peptide (PEP3) (chains D)
GGGGGAPTAKAPSK

Primary citation

Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization. Ting, Y.T., Harris, P.W., Batot, G. et al. IUCrJ (2016) 3:10-19. DOI 10.1107/S2052252515019971 · PubMed

Other PDB entries of the same protein (UniProt P0AEY0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PQP 1.07 Å, Crystal structure of maltose binding protein (Apo), mutant Trp340 to 4-Fluorotryptophan
9PQL 1.37 Å, Crystal structure of maltose binding protein (Apo), mutant Trp62 to 4-Fluorotryptophan
9PQN 1.37 Å, Crystal structure of maltose binding protein (Apo), mutant Trp340 to 4-Cyanotryptophan
9TY2 1.75 Å, Crystal structure of a Picomolar Nanobody in complex with Maltose Binding Protein, MBP,…
4WGI 1.85 Å, A Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia…
9PQK 1.87 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Fluorotryptophan
4WVI 1.9 Å, Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in…
4YS9 2.0 Å, Ataxin-3 Carboxy-Terminal Region - Crystal C1 (tetragonal)
5II4 2.0 Å, Crystal structure of red abalone VERL repeat 1 with linker at 2.0 A resolution
5JON 2.04 Å, Crystal structure of the unliganded form of HCN2 CNBD
4WVG 2.05 Å, Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB).
3VD8 2.07 Å, Crystal structure of human AIM2 PYD domain with MBP fusion

Browse structure collections

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