6BJ5

Structure of the Clinically used Myxomaviral Serine Protease Inhibitor 1 (SERP-1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history. 


Literature

Structure of the Clinically used Myxomaviral Serine Protease Inhibitor 1 (SERP-1)

Mahon, B.P., Lomelino, C.L., Ambadapadi, S., Yaron, J., Keinan, S., Kurnikov, I., Zhang, L., Reeves, W., Pinard, M.A., Macaulay, C., McFadden, G., Tibbetts, S., McKenna, R., Lucas, A.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine proteinase inhibitor 1A [auth B],
C [auth A],
E [auth C]		315Myxoma virus (strain Lausanne)Mutation(s): 0 
Gene Names: SPI-1, SERP1, m008.1L
UniProt
Find proteins for P12393 (Myxoma virus (strain Lausanne))
Explore P12393 
Go to UniProtKB:  P12393
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12393
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine proteinase inhibitor 1B [auth F],
D [auth G],
F [auth H]		54Myxoma virus (strain Lausanne)Mutation(s): 0 
Gene Names: SPI-1, SERP1, m008.1L
UniProt
Find proteins for P12393 (Myxoma virus (strain Lausanne))
Explore P12393 
Go to UniProtKB:  P12393
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12393
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D],
H [auth E]		2N/A
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P15
Query on P15
Download Ideal Coordinates CCD File 
J [auth C]2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
C13 H28 O7
FHHGCKHKTAJLOM-UHFFFAOYSA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
I [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.012α = 90
b = 122.066β = 94.88
c = 130.095γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM109524

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary