6Q2M: Photinus pyralis Luciferase Pps6 mutant

Crystal structure of Photinus pyralis Luciferase Pps6 mutant in complex with DLSA. Determined by X-ray diffraction at 2.75 Å resolution. Released 16 Oct 2019.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Photinus pyralis
Chains: 3
Atoms: 11,968
Mol. weight: 188.99 kDa
Ligands: DYD, SLU
Released: 16 Oct 2019

Explore 6Q2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q2M contains 80 α-helices and 86 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: 31 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	8-9	2	1
α-helix	10-13	4
α-helix	16-19	4
α-helix	22-34	13
β-strand	40-44	5	2
β-strand	49-52	4	2
α-helix	53-70	18
β-strand	77-81	5	3
α-helix	89-97	9
β-strand	101-104	4	3
α-helix	111-121	11
β-strand	125-128	4	3
α-helix	130-140	11
β-strand	148-151	4	3
β-strand	158	1	4
β-strand	161	1	4
β-strand	162-163	2	3
α-helix	164-171	8
α-helix	172-173	2
α-helix	178-180	3
β-strand	192-197	6	3
α-helix	198	1
β-strand	207-211	5	3
α-helix	212-222	11
β-strand	236-239	4	2
α-helix	246-257	12
β-strand	261-264	4	2
α-helix	270-279	10
β-strand	282-287	6	2
α-helix	289-291	3
α-helix	293-296	4
α-helix	301-303	3
β-strand	311-315	5	2
α-helix	321-330	10
β-strand	336-341	6	2
α-helix	343-345	3
β-strand	348-351	4	2
α-helix	352-353	2
β-strand	363	1	1
β-strand	364-365	2	2
α-helix	366	1
β-strand	370-374	5	1
α-helix	380	1
β-strand	381	1	1
α-helix	382	1
β-strand	388-393	6	1
β-strand	400-401	2	3
α-helix	405-411	7
β-strand	412	1	1
β-strand	418-426	9	1
β-strand	432-437	6	1
α-helix	438-440	3
β-strand	442-443	2	5
β-strand	448-449	2	5
α-helix	450	1
α-helix	451-460	10
β-strand	464-474	11	6
β-strand	478-487	10	6
α-helix	488	1
α-helix	495-503	9
β-strand	516-518	3	6
β-strand	524	1	7
β-strand	530	1	7
α-helix	532-538	7

Chain B: 28 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	8-9	2	8
α-helix	10-13	4
α-helix	16-19	4
α-helix	22-34	13
β-strand	40-44	5	9
β-strand	49-52	4	9
α-helix	53-70	18
β-strand	77-81	5	10
α-helix	89-98	10
β-strand	101-104	4	10
α-helix	111-121	11
β-strand	125-128	4	10
α-helix	130-140	11
β-strand	148-151	4	10
β-strand	158	1	11
β-strand	161	1	11
β-strand	162-163	2	10
α-helix	164-171	8
α-helix	172-173	2
α-helix	178-180	3
β-strand	192-197	6	10
α-helix	198	1
β-strand	207-211	5	10
α-helix	212-222	11
β-strand	236-239	4	9
α-helix	246-257	12
β-strand	261-264	4	9
α-helix	270-279	10
β-strand	284-287	4	9
α-helix	290-296	7
α-helix	301-303	3
β-strand	311-315	5	9
α-helix	321-330	10
β-strand	337-341	5	9
α-helix	343-345	3
β-strand	348-351	4	9
α-helix	352-353	2
β-strand	363	1	8
β-strand	364-365	2	9
α-helix	366	1
β-strand	370-374	5	8
α-helix	380	1
β-strand	381	1	8
α-helix	382	1
β-strand	388-393	6	8
β-strand	400-401	2	10
α-helix	405-411	7
β-strand	412	1	8
β-strand	418-426	9	8
β-strand	432-437	6	8
α-helix	438-440	3
α-helix	451-458	8
α-helix	498-500	3
α-helix	501-504	4

Chain C: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
β-strand	8-9	2	12
α-helix	10-13	4
α-helix	16-19	4
α-helix	22-33	12
β-strand	40-44	5	13
β-strand	49-52	4	13
α-helix	53-70	18
β-strand	77-81	5	14
α-helix	89-97	9
β-strand	101-104	4	14
α-helix	111-121	11
β-strand	125-128	4	14
α-helix	130-140	11
β-strand	148-151	4	14
β-strand	162-163	2	14
α-helix	164-171	8
α-helix	172-173	2
α-helix	178-180	3
β-strand	192-198	7	14
α-helix	203-205	3
β-strand	206-211	6	14
α-helix	212-223	12
β-strand	236-239	4	13
α-helix	246-257	12
β-strand	261-264	4	13
α-helix	272-279	8
β-strand	284-287	4	13
α-helix	290-294	5
α-helix	300-303	4
β-strand	311-315	5	13
α-helix	321-330	10
β-strand	337-341	5	13
α-helix	343-345	3
β-strand	348-351	4	13
β-strand	364-365	2	13
α-helix	366	1
β-strand	370-374	5	12
β-strand	381	1	12
β-strand	388-393	6	12
β-strand	400-401	2	14
α-helix	405-411	7
β-strand	412	1	12
β-strand	418-426	9	12
β-strand	431	1	13
β-strand	432-437	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Luciferin 4-monooxygenase	A, B, C	protein	555	Photinus pyralis	P08659 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6Q2M_1 Luciferin 4-monooxygenase (chains A, B, C)
GPLGSMEDAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAE
YFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPANDIYNERELL
NSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPG
FNEYDFVPESFDRDKTIALIMNSSGSTGLPKGVALPHRNACVRFSHCRDPIFGNQIIPDT
AILSVVPFHHGFGMFTTLGFLICGFRVVLMYRFEEELFLRTLQDYKIQSALLVPTLFSFF
AKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFNLPGIRQGYGLTETTSAILITPNG
DDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSGYVNNPEATNALIDKD
GWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILLQHPNIFDAGVAGLPDD
DAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKI
REILIKAKKGGKSKL

Ligands and cofactors

ID	Name	Formula	Copies
DYD	(2S,5S)-hexane-2,5-diol	C6 H14 O2	4
SLU	5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine	C21 H18 N8 O8 S3	3

Water and common crystallization additives (SO4, EDO) are not listed.

Primary citation

Mutagenesis and Structural Studies Reveal the Basis for the Activity and Stability Properties That Distinguish thePhotinusLuciferasesscintillansandpyralis. Branchini, B.R., Fontaine, D.M., Southworth, T.L. et al. Biochemistry (2019) 58:4293-4303. DOI 10.1021/acs.biochem.9b00719 · PubMed

Other PDB entries of the same protein (UniProt P08659 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RIX 1.7 Å, 1.7A resolution structure of a firefly luciferase-Aspulvinone J inhibitor complex
1LCI 2.0 Å, Firefly luciferase
3IES 2.0 Å, Firefly luciferase inhibitor complex
5GZ2 2.0 Å, luciferase complex with 7-cy-L
5KYT 2.0 Å, Structure of Photinus pyralis Luciferase red light emitting variant
3IER 2.05 Å, Firefly luciferase apo structure (P41 form) with PEG 400 bound
3IEP 2.1 Å, Firefly luciferase apo structure (P41 form)
1BA3 2.2 Å, Firefly luciferase in complex with bromoform
4E5D 2.2 Å, 2.2A resolution structure of a firefly luciferase-benzothiazole inhibitor complex
5DWV 2.3 Å, Crystal structure of the Luciferase complexed with substrate analogue
4G37 2.4 Å, Structure of cross-linked firefly luciferase in second catalytic conformation
5DV9 2.4 Å, Crystal structure of the Luciferase

Browse structure collections

About this viewer

MolViewer shows 6Q2M 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.