7WHU | pdb_00007whu

Human Neutrophil Elastase in-complex with Ecotin Peptide

PDB DOI: https://doi.org/10.2210/pdb7WHU/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-12-31 Released: 2022-07-06
Deposition Author(s): Shankar, S., Jayaraman, S.
Funding Organization(s): Ministry of Education (MoE, Singapore)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.306 (Depositor), 0.310 (DCC)
R-Value Work:
0.252 (Depositor), 0.252 (DCC)
R-Value Observed:
0.270 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Sequence preference and scaffolding requirement for the inhibition of human neutrophil elastase by ecotin peptide

Bagga, T., Loh, S.N., Sivaraman, J., Shankar, S.

(2022) Protein Sci 31: 933-941

DOI: https://doi.org/10.1002/pro.4274

Macromolecule Content

Total Structure Weight: 122.83 kDa
Atom Count: 7,019
Modeled Residue Count: 904
Deposited Residue Count: 1,100
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil elastase	A [auth D], B [auth A], C [auth B], D [auth C]	267	Homo sapiens	Mutation(s): 0 Gene Names: ELANE, ELA2 EC: 3.4.21.37
UniProt & NIH Common Fund Data Resources
Find proteins for P08246 (Homo sapiens) Explore P08246 Go to UniProtKB: P08246
PHAROS: P08246 GTEx: ENSG00000197561
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08246
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth D] Focus chain B [auth A] Focus chain C [auth B] Focus chain D [auth C]	Go to GlyGen: P08246-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ecotin Peptide	E, F, G, H	8	Homo sapiens	Mutation(s): 0

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth P], L [auth K], O [auth N], P [auth O]	3		N-Glycosylation	Interactions Focus chain I [auth P] Focus chain L [auth K] Focus chain O [auth N] Focus chain P [auth O] Interactions & Density Focus chain I [auth P] Focus chain L [auth K] Focus chain O [auth N] Focus chain P [auth O]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I]	2		N-Glycosylation	Interactions Focus chain J [auth I] Interactions & Density Focus chain J [auth I]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J]	4		N-Glycosylation	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth L]	2		N-Glycosylation	Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	N [auth M]	3		N-Glycosylation	Interactions Focus chain N [auth M] Interactions & Density Focus chain N [auth M]
Glycosylation Resources
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain R [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth D] mmCIF format, chain AA [auth C]	AA [auth C], R [auth D], T [auth B], U [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain R [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain R [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain Q [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth D]	Q [auth D] S [auth A] V [auth B] W [auth B] X [auth B] Q [auth D], S [auth A], V [auth B], W [auth B], X [auth B], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Interactions & Density Focus chain Q [auth D] Focus chain S [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C]