6BJ5 | pdb_00006bj5

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

PDB DOI: https://doi.org/10.2210/pdb6BJ5/pdb

Classification: IMMUNOSUPPRESSANT
Organism(s): Myxoma virus (strain Lausanne)
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2017-11-05 Released: 2018-11-07
Deposition Author(s): Mahon, B.P., Lomelino, C.L., McKenna, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.257 (Depositor), 0.261 (DCC)
R-Value Work:
0.207 (Depositor), 0.211 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

Macromolecule Content

Total Structure Weight: 126.23 kDa
Atom Count: 8,023
Modeled Residue Count: 990
Deposited Residue Count: 1,107
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine proteinase inhibitor 1	A [auth B], C [auth A], E [auth C]	315	Myxoma 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12393
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth A]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine proteinase inhibitor 1	B [auth F], D [auth G], F [auth H]	54	Myxoma 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12393
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D], H [auth E]	2		N/A	Interactions Focus chain G [auth D] Focus chain H [auth E] Interactions & Density Focus chain G [auth D] Focus chain H [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P15 Query on P15 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.257 (Depositor), 0.261 (DCC)
R-Value Work: 0.207 (Depositor), 0.211 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.012	α = 90
b = 122.066	β = 94.88
c = 130.095	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-07

Deposition Author(s):

Mahon, B.P.

Lomelino, C.L.

McKenna, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM109524

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