9ATK: Neutrophil elastase

BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap4 of S. aureus. Determined by X-ray diffraction at 2.11 Å resolution. Released 12 Jun 2024.

Method: X-ray diffraction
Resolution: 2.11 Å
Organisms: Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
Chains: 12
Atoms: 17,989
Mol. weight: 250.34 kDa
Ligands: NAG
Released: 12 Jun 2024

Explore 9ATK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ATK contains 84 α-helices and 224 β-strands across 12 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: 11 helices, 25 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	96-98	3	3
β-strand	100-105	6	3
β-strand	109	1	5
β-strand	114	1	5
β-strand	118-122	5	3
α-helix	126-128	3
β-strand	129	1	6
β-strand	132	1	6
α-helix	134-136	3
α-helix	138-139	2
α-helix	144-145	2
β-strand	149-154	6	2
β-strand	157	1	7
α-helix	163	1
β-strand	164	1	7
α-helix	165	1
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	210-217	8	2
β-strand	218-219	2	8
β-strand	229-233	5	2
α-helix	234-237	4
α-helix	238-245	8

Chain B: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	42
β-strand	20-21	2	43
α-helix	22-23	2
β-strand	30-37	8	17
β-strand	40-50	11	17
β-strand	53-56	4	17
α-helix	58-60	3
β-strand	64-69	6	17
β-strand	73	1	44
β-strand	82-91	10	17
β-strand	96	1	45
β-strand	101	1	45
β-strand	105-109	5	17
β-strand	116	1	46
β-strand	119	1	46
β-strand	123	1	43
α-helix	124-126	3
β-strand	136-141	6	43
β-strand	153	1	44
β-strand	155-161	7	43
α-helix	162-163	2
α-helix	164-170	7
β-strand	179-182	4	43
β-strand	190	1	42
α-helix	198	1
β-strand	199-202	4	43
β-strand	205-212	8	43
β-strand	213-214	2	18
α-helix	218	1
α-helix	220	1
β-strand	221-225	5	43
α-helix	226-229	4
α-helix	230-237	8

Chain C: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	373-375	3	17
β-strand	376-380	5	18
β-strand	383-384	2	18
β-strand	388-392	5	17
β-strand	399	1	19
α-helix	401-416	16
α-helix	420-425	6
β-strand	429-435	7	18
β-strand	440-444	5	18
β-strand	449-450	2	8
β-strand	455	1	19
α-helix	457-459	3
β-strand	460-467	8	18

Chain D: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	9
β-strand	33-34	2	10
α-helix	35-36	2
β-strand	43-47	5	11
β-strand	52-60	9	11
β-strand	63-66	4	11
α-helix	68-71	4
α-helix	76-78	3
β-strand	80-83	4	11
β-strand	87	1	12
β-strand	96-98	3	11
β-strand	100-105	6	11
β-strand	109	1	13
β-strand	114	1	13
β-strand	118-122	5	11
β-strand	129	1	14
β-strand	132	1	14
α-helix	144-145	2
β-strand	149-154	6	10
β-strand	157	1	15
α-helix	163	1
β-strand	164	1	15
α-helix	165	1
β-strand	167	1	12
β-strand	169-176	8	10
β-strand	185-188	4	10
β-strand	195	1	9
β-strand	204-207	4	10
β-strand	210-217	8	10
β-strand	218-219	2	16
β-strand	229-233	5	10
α-helix	234-237	4
α-helix	238-245	8

Chain E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	20
β-strand	20-21	2	21
α-helix	22-23	2
β-strand	30-37	8	22
β-strand	40-50	11	22
β-strand	53-56	4	22
α-helix	58-60	3
β-strand	64-69	6	22
β-strand	73	1	23
β-strand	82-91	10	22
β-strand	96	1	24
β-strand	101	1	24
β-strand	105-109	5	22
β-strand	116	1	25
β-strand	119	1	25
β-strand	136-141	6	21
β-strand	153	1	23
β-strand	155-161	7	21
α-helix	164-170	7
β-strand	179-182	4	21
β-strand	190	1	20
β-strand	199-202	4	21
β-strand	205-212	8	21
β-strand	213-214	2	26
α-helix	218	1
α-helix	220	1
β-strand	221-225	5	21
α-helix	226-229	4
α-helix	230-236	7

Chain F: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	372-375	4	22
β-strand	376-380	5	26
β-strand	383-384	2	26
β-strand	388-393	6	22
β-strand	399	1	27
α-helix	401-416	16
α-helix	420-425	6
β-strand	429-435	7	26
β-strand	440-444	5	26
β-strand	449-450	2	16
β-strand	455	1	27
α-helix	457-459	3
β-strand	460-467	8	26

Chain G: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	28
β-strand	33-34	2	29
α-helix	35-36	2
β-strand	43-47	5	30
β-strand	52-60	9	30
β-strand	63-66	4	30
α-helix	68-71	4
α-helix	76-78	3
β-strand	80-83	4	30
β-strand	87	1	31
β-strand	96-105	10	30
β-strand	109	1	32
β-strand	114	1	32
β-strand	118-122	5	30
α-helix	126-128	3
β-strand	149-154	6	29
α-helix	163-165	3
β-strand	167	1	31
α-helix	168	1
β-strand	169-176	8	29
β-strand	185-188	4	29
β-strand	195	1	28
β-strand	204-207	4	29
β-strand	210-217	8	29
β-strand	218-219	2	33
β-strand	229-233	5	29
α-helix	234-237	4
α-helix	238-245	8

Chain H: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	34
β-strand	20-21	2	35
α-helix	22-23	2
β-strand	30-37	8	36
β-strand	40-50	11	36
β-strand	53-56	4	36
α-helix	58-60	3
β-strand	64-69	6	36
β-strand	73	1	37
β-strand	82-91	10	36
β-strand	96	1	38
β-strand	101	1	38
β-strand	105-109	5	36
β-strand	116	1	39
β-strand	119	1	39
α-helix	121-122	2
β-strand	123	1	35
α-helix	124-126	3
β-strand	136-141	6	35
β-strand	146	1	40
β-strand	149	1	40
β-strand	153	1	37
β-strand	155-161	7	35
α-helix	164-168	5
β-strand	179-182	4	35
β-strand	190	1	34
α-helix	198	1
β-strand	199-202	4	35
β-strand	205-212	8	35
β-strand	213-214	2	36
α-helix	218	1
α-helix	220	1
β-strand	221-225	5	35
α-helix	226-228	3
α-helix	230-236	7

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neutrophil elastase	A, D, G, J	protein	218	Homo sapiens	P08246 (AlphaFold model)
Extracellular Adherence Protein	C, F, I, L	protein	108	Staphylococcus aureus subsp. aureus Mu50	Q99QS1 (AlphaFold model)
Cathepsin-G	B, E, H, K	protein	223	Homo sapiens	P08311 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>9ATK_1 Neutrophil elastase (chains A, D, G, J)
IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNL
SRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGV
QCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCN
GLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ

Sequence of entity 2 (C, F, I, L), FASTA

>9ATK_2 Extracellular Adherence Protein (chains C, F, I, L)
GSTRYVPYTIAVNGTSTPILSKLKISNKQLISYKYLNDKVKSVLKSERGISDLDLKFAKQ
AKYTVYFKNGKKQVVNLKSDIFTPNLFSAKDIKKIDIDVKQYTKSKKK

Sequence of entity 3 (B, E, H, K), FASTA

>9ATK_3 Cathepsin-G (chains B, E, H, K)
IIGGRESRPHSRPYMAYLQIQSPAGQSRCGGFLVREDFVLTAAHCWGSNINVTLGAHNIQ
RRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRVRRNRNVNPVALPRAQEGLRPGT
LCTVAGWGRVSMRRGTDTLREVQLRVQRDRQCLRIFGSYDPRRQICVGDRRERKAAFKGD
SGGPLLCNNVAHGIVSYGKSSGVPPEVFTRVSSFLPWIRTTMR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases. Mishra, N., Gido, C.D., Herdendorf, T.J. et al. J Biol Chem (2024) 300:107627-107627. DOI 10.1016/j.jbc.2024.107627 · 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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