3WOL: DAP BII dipeptide complex I

Crystal structure of the DAP BII dipeptide complex I. Determined by X-ray diffraction at 1.74 Å resolution. Released 3 Sept 2014.

Method: X-ray diffraction
Resolution: 1.74 Å
Organism: Pseudoxanthomonas mexicana
Chains: 2
Atoms: 12,085
Mol. weight: 154.25 kDa
Ligands: VAL, TYR, ZN
Released: 3 Sept 2014

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

Secondary structure: helices and β-sheets

3WOL contains 80 α-helices and 50 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: 40 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	1
α-helix	31-33	3
α-helix	34-44	11
α-helix	50-54	5
α-helix	61-63	3
β-strand	64-66	3	2
β-strand	71-74	4	2
β-strand	80-83	4	2
α-helix	85-94	10
α-helix	102-105	4
β-strand	107-108	2	2
α-helix	112-114	3
α-helix	115	1
β-strand	116-117	2	2
β-strand	124-132	9	2
α-helix	134-142	9
α-helix	148-166	19
β-strand	172-179	8	2
β-strand	184-193	10	2
β-strand	195-201	7	2
α-helix	204-207	4
α-helix	211-214	4
β-strand	226-232	7	2
β-strand	246-247	2	2
β-strand	256	1	1
β-strand	266-271	6	1
α-helix	282-287	6
α-helix	288-292	5
α-helix	293-313	21
α-helix	315-320	6
α-helix	322-345	24
α-helix	347-363	17
α-helix	366-369	4
α-helix	370-387	18
α-helix	390-399	10
α-helix	403-417	15
α-helix	422-424	3
α-helix	431-433	3
α-helix	434-443	10
α-helix	444-446	3
α-helix	450-465	16
α-helix	469-471	3
α-helix	474-480	7
α-helix	485-496	12
α-helix	503-511	9
α-helix	514-518	5
α-helix	523-566	44
β-strand	580-586	7	1
β-strand	589	1	3
β-strand	595-597	3	3
β-strand	600-602	3	1
α-helix	603-608	6
β-strand	613	1	4
β-strand	616	1	4
α-helix	620-627	8
β-strand	636	1	5
β-strand	641	1	5
β-strand	643-648	6	1
α-helix	659	1
β-strand	660-662	3	1
β-strand	668-675	8	1
α-helix	677-683	7
α-helix	688-690	3
β-strand	693-697	5	1
α-helix	698-707	10
α-helix	712-717	6

Chain B: 40 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	6
α-helix	31-33	3
α-helix	34-44	11
α-helix	50-53	4
α-helix	61-63	3
β-strand	64-66	3	7
β-strand	71-74	4	7
β-strand	80-83	4	7
α-helix	85-94	10
α-helix	102-105	4
β-strand	107-108	2	7
α-helix	112-114	3
α-helix	115	1
β-strand	116-117	2	7
β-strand	124-132	9	7
α-helix	134-143	10
α-helix	148-166	19
β-strand	172-179	8	7
β-strand	184-193	10	7
β-strand	195-201	7	7
α-helix	204-207	4
α-helix	211-214	4
β-strand	226-232	7	7
β-strand	246-247	2	7
β-strand	256	1	6
β-strand	266-271	6	6
α-helix	282-287	6
α-helix	288-292	5
α-helix	293-312	20
α-helix	315-320	6
α-helix	322-345	24
α-helix	347-363	17
α-helix	370-388	19
α-helix	390-401	12
α-helix	403-417	15
α-helix	422-424	3
α-helix	431-433	3
α-helix	434-443	10
α-helix	444-446	3
α-helix	450-465	16
α-helix	469-471	3
α-helix	474-480	7
α-helix	485-495	11
α-helix	503-510	8
α-helix	514-518	5
α-helix	523-566	44
α-helix	573-575	3
β-strand	580-586	7	6
β-strand	589	1	3
β-strand	595-597	3	3
β-strand	600-602	3	6
α-helix	603-608	6
α-helix	620-627	8
β-strand	636	1	8
β-strand	641	1	8
β-strand	643-648	6	6
α-helix	659	1
β-strand	660-662	3	6
β-strand	668-675	8	6
α-helix	677-683	7
α-helix	688-690	3
β-strand	693-697	5	6
α-helix	698-707	10
α-helix	712-717	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
dipeptidyl aminopeptidase BII	A, B	protein	698	Pseudoxanthomonas mexicana	V5YM14 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3WOL_1 dipeptidyl aminopeptidase BII (chains A, B)
GEGMWVPQQLPEIAGPLKKAGLKLSPQQISDLTGDPMGAVVALGGCTASFVSPNGLVVTN
HHCAYGAIQLNSTAENNLIKNGFNAPTTADEVSAGPNARVFVLDEITDVTKDAKAAIAAA
GDDALARTKALEAFEKKLIADCEAEAGFRCRLYSFSGGNTYRLFKNLEIKDVRLAYAPPG
SVGKFGGDIDNWMWPRHTGDFAFYRAYVGKDGKPAAFSKDNVPYQPKHWLKFADQPLGAG
DFVMVAGYPGSTNRYALAAEFDNTAQWTYPTIARHYKNQIAMVEAAGKQNADIQVKYAAT
MAGWNNTSKNYDGQLEGFKRIDAAGQKLREEAAVLGWLKGQGAKGQPALDAHAKLLDLLE
QSKATRDRDLTLALFNNTAMLGSATQLYRLSIEREKPNAERESGYQERDLPAIEGGLKQL
ERRYVAAMDRQLQEYWLNEYIKLPADQRVAAVDAWLGGNDAAAVKRALDRLAGTKLGSTE
ERLKWFAADRKAFEASNDPAIQYAVAVMPTLLKLEQERKTRAGENLAARPVYLQALADYK
KSQGEFVYPDANLSLRITFGNVMGYAPKDGMEYTPFTTLEGVVAKETGQDPFDSPKALLD
AVAAKRYGGLEDKRIGSVPVNYLSDLDITGGNSGSPVLDAHGKLVGLAFDGNWESVSSNW
VFDPKMTRMIAVDGRYLRWIMQEVYPAPQLLKEMNVGK

Ligands and cofactors

ID	Name	Formula	Copies
VAL	Valine	C5 H11 N O2	2
TYR	Tyrosine	C9 H11 N O3	2
ZN	Zinc ion	Zn	5

Water and common crystallization additives (GOL) are not listed.

Primary citation

S46 peptidases are the first exopeptidases to be members of clan PA. Sakamoto, Y., Suzuki, Y., Iizuka, I. et al. Sci Rep (2014) 4:4977-4977. DOI 10.1038/srep04977 · PubMed

Other PDB entries of the same protein (UniProt V5YM14 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3WON 1.75 Å, Crystal structure of the DAP BII dipeptide complex III
3WOO 1.8 Å, Crystal structure of the DAP BII hexapeptide complex I
3WOQ 1.82 Å, Crystal structure of the DAP BII hexapeptide complex III
3WOM 1.86 Å, Crystal structure of the DAP BII dipeptide complex II
3WOK 1.95 Å, Crystal structure of the DAP BII (Space)
3WOP 1.95 Å, Crystal structure of the DAP BII hexapeptide complex II
3WOI 2.1 Å, Crystal structure of the DAP BII (S657A)
3WOR 2.1 Å, Crystal structure of the DAP BII octapeptide complex
4Y06 2.18 Å, Crystal structure of the DAP BII (G675R) dipeptide complex
3WOJ 2.2 Å, Crystal structure of the DAP BII

Browse structure collections

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