8D4U: Neutrophil elastase

Crystal Structure of Neutrophil Elastase Inhibited by Eap2 from S. aureus. Determined by X-ray diffraction at 1.9 Å resolution. Released 21 Dec 2022.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Staphylococcus aureus subsp. aureus
Chains: 4
Atoms: 5,216
Mol. weight: 70.05 kDa
Ligands: NAG
Released: 21 Dec 2022

Explore 8D4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D4U contains 26 α-helices and 59 β-strands across 4 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	1
β-strand	33-34	2	2
α-helix	35-36	2
β-strand	43-48	6	3
β-strand	51-60	10	3
β-strand	63-66	4	3
α-helix	68-71	4
α-helix	76-78	3
β-strand	80-83	4	3
β-strand	87	1	4
β-strand	96-105	10	3
β-strand	109	1	5
β-strand	114	1	5
β-strand	118-122	5	3
α-helix	126-128	3
α-helix	134-136	3
α-helix	144-145	2
β-strand	149-154	6	2
β-strand	157	1	6
β-strand	164	1	6
β-strand	167	1	4
β-strand	169-176	8	2
β-strand	185-188	4	2
β-strand	195	1	1
β-strand	204-207	4	2
β-strand	210-219	10	2
α-helix	228	1
β-strand	229-233	5	2
α-helix	234-237	4
α-helix	238-245	8

Chain B: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	9
β-strand	33-34	2	10
α-helix	35-36	2
β-strand	43-48	6	11
β-strand	51-60	10	11
β-strand	63-66	4	11
α-helix	68-70	3
α-helix	76-78	3
β-strand	80-83	4	11
β-strand	87	1	12
β-strand	96-104	9	11
β-strand	109	1	13
β-strand	114	1	13
β-strand	118-122	5	11
α-helix	126-128	3
α-helix	134-137	4
α-helix	144-145	2
β-strand	149-154	6	10
β-strand	157	1	14
β-strand	164	1	14
β-strand	167	1	12
α-helix	168	1
β-strand	169-176	8	10
β-strand	185-188	4	10
β-strand	195	1	9
α-helix	203	1
β-strand	204-207	4	10
β-strand	210-219	10	10
α-helix	228	1
β-strand	229-233	5	10
α-helix	234-236	3
α-helix	238-245	8

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	159-166	8	7
β-strand	175-178	4	7
β-strand	184-185	2	8
α-helix	187-202	16
α-helix	206-211	6
β-strand	215-221	7	7
β-strand	226-230	5	7
β-strand	235-237	3	2
β-strand	241-242	2	8
α-helix	243-245	3
β-strand	246-253	8	7

Chain D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	161-166	6	15
β-strand	169	1	15
β-strand	175-176	2	15
β-strand	184-185	2	16
α-helix	187-202	16
α-helix	206-211	6
β-strand	215-221	7	15
β-strand	226-230	5	15
β-strand	235-237	3	10
β-strand	241-242	2	16
α-helix	243-245	3
β-strand	246-253	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil elastase	A, B	protein	218	Homo sapiens	P08246 (AlphaFold model)
Extracellular Adherence Protein	C, D	protein	100	Staphylococcus aureus subsp. aureus	Q99QS1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8D4U_1 Neutrophil elastase (chains A, B)
IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNL
SRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGV
QCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCN
GLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ

Sequence of entity 2 (C, D), FASTA

>8D4U_2 Extracellular Adherence Protein (chains C, D)
GSTVQVPYTITVNGTSQNILSNLTFNKNQNISYKDLEGKVKSVLESNRGITDVDLRLSKQ
AKYTVNFKNGTKKVIDLKSGIYTANLINSSDIKSININVD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Characterization of two distinct neutrophil serine protease-binding modes within a Staphylococcus aureus innate immune evasion protein family. Gido, C.D., Herdendorf, T.J., Geisbrecht, B.V. J Biol Chem (2023) 299:102969-102969. DOI 10.1016/j.jbc.2023.102969 · PubMed

Other PDB entries of the same protein (UniProt P08246 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SI4 1.14 Å, Structure of human neutrophil elastase in complex with a…
8VK5 1.56 Å, Human Sputum Leucocyte Elastase (uncomplexed)
5ABW 1.6 Å, Neutrophil elastase inhibitors for the treatment of (cardio)pulmonary diseases
4WVP 1.63 Å, Crystal structure of an activity-based probe HNE complex
2Z7F 1.7 Å, Crystal structure of the complex of human neutrophil elastase with 1/2SLPI
9ASS 1.75 Å, Crystal Structure of Neutrophil Elastase Inhibited by Eap4 from S. aureus
5A0A 1.78 Å, Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone…
1PPF 1.8 Å, X-ray crystal structure of the complex of human leukocyte elastase (pmn elastase) and…
2RG3 1.8 Å, Covalent complex structure of elastase
8G25 1.8 Å, Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at…
5A09 1.81 Å, Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone…
8G24 1.82 Å, Crystal Structure of Cathepsin-G and Neutrophil Elastase Inhibited by S. aureus EapH2 at…

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