5DV9: Luciferase

Crystal structure of the Luciferase. Determined by X-ray diffraction at 2.4 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Photinus pyralis
Chains: 1
Atoms: 4,421
Mol. weight: 63.37 kDa
Released: 28 Sept 2016

Explore 5DV9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DV9 contains 28 α-helices and 36 β-strands across 1 chain. 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: 28 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	1
α-helix	16-18	3
α-helix	22-34	13
β-strand	40-44	5	2
β-strand	50-52	3	2
α-helix	53-70	18
β-strand	77-81	5	3
α-helix	89-97	9
β-strand	101-105	5	3
α-helix	111-121	11
β-strand	125-128	4	3
α-helix	130-132	3
α-helix	133-140	8
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	183-185	3
β-strand	192-197	6	3
α-helix	205-206	2
β-strand	207-211	5	3
α-helix	212-223	12
β-strand	236-240	5	2
α-helix	246-257	12
β-strand	261-264	4	2
α-helix	270-279	10
β-strand	284-287	4	2
α-helix	289-297	9
α-helix	301-303	3
β-strand	311-313	3	2
α-helix	321-330	10
β-strand	337	1	2
β-strand	339-340	2	5
α-helix	343-345	3
β-strand	350-351	2	5
α-helix	352-353	2
β-strand	363	1	1
β-strand	364-365	2	5
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	405-409	5
β-strand	412	1	1
β-strand	418-426	9	1
β-strand	432-434	3	1
α-helix	437-439	3
β-strand	442-444	3	6
β-strand	447-449	3	6
α-helix	451-459	9
β-strand	464-473	10	7
β-strand	478	1	6
β-strand	479-487	9	7
α-helix	488	1
α-helix	495-503	9
α-helix	508-510	3
β-strand	515-518	4	7
β-strand	524	1	8
β-strand	530	1	8
α-helix	532-542	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Luciferin 4-monooxygenase	A	protein	573	Photinus pyralis	P08659 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5DV9_1 Luciferin 4-monooxygenase (chains A)
MGSSHHHHHHSQDLEVLFQGPGSMEDAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVP
GTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALF
IGVAVAPANDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTD
YQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSGSTGLPKGVALPHRTACV
RFSHARDPIFGNQIIPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSL
QDYKIQSALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIR
QGYGLTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMI
MSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESI
LLQHPNIFDAGVAGLPDDDAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVV
FVDEVPKGLTGKLDARKIREILIKAKKGGKSKL

Primary citation

Crystal structure of the Luciferase. Su, J., Li, Z., Yuan, Z. et al. To be published.

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
5GYZ 2.4 Å, luciferase AMP/7-cy-L complex

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