7CBK: Human Neutrophil Elastase Ecotin complex

Structure of Human Neutrophil Elastase Ecotin complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Escherichia coli K-12, Homo sapiens
Chains: 4
Atoms: 5,656
Mol. weight: 95.77 kDa
Ligands: NAG, MG
Released: 12 Aug 2020

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

Secondary structure: helices and β-sheets

7CBK contains 29 α-helices and 66 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: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
β-strand	20-26	7	1
α-helix	27-29	3
α-helix	33-35	3
β-strand	36-48	13	2
β-strand	53-54	2	3
β-strand	55	1	4
β-strand	58-64	7	1
β-strand	69-75	7	1
α-helix	78-80	3
β-strand	81-83	3	3
α-helix	85-87	3
β-strand	93-98	6	2
β-strand	99	1	4
α-helix	102-105	4
β-strand	106-108	3	2
β-strand	114-120	7	1
β-strand	124-138	15	2
β-strand	140-141	2	5

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	12
β-strand	20-21	2	3
α-helix	22-23	2
β-strand	30-35	6	13
β-strand	39-48	10	13
β-strand	51-54	4	13
α-helix	56-58	3
α-helix	62B-64	3
β-strand	65-68	5	13
β-strand	72	1	14
β-strand	81-89	9	13
β-strand	96	1	15
β-strand	100	1	15
β-strand	104-108	5	13
α-helix	112-114	3
β-strand	115	1	16
β-strand	118	1	16
α-helix	120-125	6
α-helix	130-131	2
β-strand	135-140	6	3
β-strand	154	1	14
β-strand	156-163	7	3
β-strand	181-184	4	3
β-strand	189	1	12
α-helix	197	1
β-strand	198-201	4	3
β-strand	208-217A	10	3
β-strand	226-230	5	3
α-helix	231-234	4
α-helix	235-242	8

Chain C: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
β-strand	20-26	7	5
α-helix	27-29	3
α-helix	33-35	3
β-strand	36-48	13	2
β-strand	53-54	2	6
β-strand	55	1	7
β-strand	58-64	7	5
β-strand	69-75	7	5
α-helix	78-80	3
β-strand	81-83	3	6
β-strand	93-98	6	2
β-strand	99	1	7
α-helix	102-105	4
β-strand	106-108	3	2
β-strand	114-120	7	5
β-strand	124-138	15	2
β-strand	140-141	2	1

Chain D: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	8
β-strand	20-21	2	6
α-helix	22-23	2
β-strand	30-35	6	9
β-strand	39-48	10	9
β-strand	51-54	4	9
α-helix	56-58	3
α-helix	62B-64	3
β-strand	65-68	5	9
β-strand	72	1	10
β-strand	81-90	10	9
β-strand	96	1	11
β-strand	100	1	11
β-strand	104-108	5	9
α-helix	112-114	3
α-helix	120-125	6
α-helix	130-131	2
β-strand	135-140	6	6
β-strand	154	1	10
β-strand	156-163	7	6
β-strand	181-184	4	6
β-strand	189	1	8
α-helix	197	1
β-strand	198-201	4	6
β-strand	208-217A	10	6
β-strand	226-230	5	6
α-helix	231-234	4
α-helix	235-242	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ecotin	A, C	protein	162	Escherichia coli K-12	P23827 (AlphaFold model)
Neutrophil elastase	B, D	protein	267	Homo sapiens	P08246 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7CBK_1 Ecotin (chains A, C)
MKTILPAVLFAAFATTSAWAAESVQPLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVEL
LIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPDGKKEKKFVTAY
LGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR

Sequence of entity 2 (B, D), FASTA

>7CBK_2 Neutrophil elastase (chains B, D)
MTLGRRLACLFLACVLPALLLGGTALASEIVGGRRARPHAWPFMVSLQLRGGHFCGATLI
APNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVI
LQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSL
CRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVN
WIDSIIQRSEDNPCPHPRDPDPASRTH

Ligands and cofactors

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

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

Primary citation

Structural Basis for the Inhibition Mechanism of Ecotin against Neutrophil Elastase by Targeting the Active Site and Secondary Binding Site. Jobichen, C., Prabhakar, M.T., Loh, S.N. et al. Biochemistry (2020) 59:2788-2795. DOI 10.1021/acs.biochem.0c00493 · PubMed

Other PDB entries of the same protein (UniProt P23827 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1SLU 1.8 Å, Rat anionic N143H, E151H trypsin complexed to A86H ecotin
1IFG 2.0 Å, Crystal structure of a monomeric form of general protease inhibitor, ecotin in absence…
1N8O 2.0 Å, Crystal structure of a complex between bovine chymotrypsin and ecotin
1SLW 2.0 Å, Rat anionic N143H, E151H trypsin complexed to A86H ecotin; nickel-bound
1ECY 2.19 Å, Protease inhibitor ecotin
1FI8 2.2 Å, Rat granzyme B [N66Q] complexed to ecotin [81-84 iepd]
1SLX 2.2 Å, Rat anionic N143H, E151H trypsin complexed to A86H ecotin; zinc-bound
1XX9 2.2 Å, Crystal Structure of the FXIa Catalytic Domain in Complex with EcotinM84R
1AZZ 2.3 Å, Fiddler crab collagenase complexed to ecotin
1EZS 2.3 Å, Crystal structure of ecotin mutant M84R, W67A, G68A, Y69A, D70A bound to rat anionic…
1SLV 2.3 Å, Rat anionic N143H, E151H trypsin complexed to A86H ecotin; copper-bound
1EZU 2.4 Å, Ecotin Y69F, D70P bound to D102N trypsin

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