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)

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Experimental Data Snapshot

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

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

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

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
SO4	E [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.216 (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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Xu, J., Rajasekaran, G., Li, S., Chen, L., Camarero, J.A.

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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  

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