7LYD: Ebola zaire Envelope glycoprotein GP

Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146. Determined by X-ray diffraction at 2.35 Å resolution. Released 24 Nov 2021.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Zaire ebolavirus
Chains: 2
Atoms: 3,123
Mol. weight: 53.62 kDa
Ligands: YOD, NAG
Released: 24 Nov 2021

Explore 7LYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LYD contains 15 α-helices and 24 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: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
β-strand	36-39	4	1
β-strand	42-45	4	1
α-helix	46-47	2
α-helix	60-62	3
β-strand	63-69	7	1
α-helix	70-73	4
α-helix	79-83	5
β-strand	86-89	4	2
β-strand	96-98	3	1
β-strand	101-103	3	1
β-strand	105-114	10	3
β-strand	120	1	3
α-helix	123-126	4
β-strand	135-144	10	3
β-strand	151-154	4	2
β-strand	159-161	3	1
β-strand	165-167	3	1
β-strand	169	1	2
α-helix	170-171	2
β-strand	176	1	3
β-strand	177-185	9	1
α-helix	186-187	2
β-strand	216-223	8	3
β-strand	231-237	7	3
β-strand	240-243	4	3
α-helix	250-263	14
β-strand	273-277	5	3
α-helix	290-292	3
β-strand	473-476	4	3

Chain B: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	503	1	1
β-strand	515-519	5	1
α-helix	539-541	3
β-strand	544-548	5	1
α-helix	551-553	3
α-helix	554-575	22
β-strand	580-581	2	1
α-helix	584-597	14
α-helix	613-628	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GP1	A	protein	291	Zaire ebolavirus	Q05320 (AlphaFold model)
GP2	B	protein	168	Zaire ebolavirus	Q05320 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7LYD_1 GP1 (chains A)
ETGRSIPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWG
FRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPC
AGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATE
DPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRS
NTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVSXXXXXX

Sequence of entity 2 (B), FASTA

>7LYD_2 GP2 (chains B)
EAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQL
ANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPADWTKNITD
KIDQIIHDFVDGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
YOD	(1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyl…	C25 H36 N2 O S	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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

Primary citation

Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146. Abendroth, J., Dranow, D.M., Lorimer, D.D. et al. To be published.

Other PDB entries of the same protein (UniProt Q05320 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2EBO 1.9 Å, Core structure of GP2 from ebola virus
6HS4 2.05 Å, Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118
6F5U 2.07 Å, Crystal structure of ebolavirus glycoprotein in complex with bepridil
6F6N 2.15 Å, Crystal structure of ebolavirus glycoprotein in complex with sertraline
6G9I 2.19 Å, Crystal structure of Ebolavirus glycoprotein in complex with clomipramine
5JQ3 2.23 Å, Crystal structure of Ebola glycoprotein
7SSQ 2.25 Å, Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound…
6G9B 2.26 Å, Crystal structure of Ebolavirus glycoprotein in complex with imipramine
7JPI 2.28 Å, Crystal structure of EBOV glycoprotein with modified HR2 stalk at 2.3A resolution
6F6S 2.29 Å, CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benztropine
6HRO 2.3 Å, Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a
6G95 2.31 Å, Crystal structure of Ebolavirus glycoprotein in complex with thioridazine

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