8VAD | pdb_00008vad

Crystal structure of MCoHNE-I, a potent in-vivo neutrophil elastase inhibitor

PDB DOI: https://doi.org/10.2210/pdb8VAD/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Momordica cochinchinensis
Mutation(s): No

Deposited: 2023-12-11 Released: 2024-12-25
Deposition Author(s): Xu, J., Rajasekaran, G., Li, S., Chen, L., Camarero, J.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.216 (Depositor), 0.214 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of MCoHNE-I, a potent in-vivo neutrophil elastase inhibitor

Rajasekaran, G., Xu, J., Li, S., Chen, L., Camarero, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 14.17 kDa
Atom Count: 1,139
Modeled Residue Count: 136
Deposited Residue Count: 136
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin inhibitor 2	A [auth B], B [auth A], C, D	34	Momordica cochinchinensis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	E [auth B], F [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE Query on NLE	A [auth B], B [auth A], C, D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.216 (Depositor), 0.214 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 16.31	α = 89.99
b = 21.227	β = 89.98
c = 70.096	γ = 67.42

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-25

Deposition Author(s):

Rajasekaran, G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM113636
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM132072

Revision History (Full details and data files)

Version 1.0: 2024-12-25
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.