5FOB

Crystal Structure of Human Complement C3b in complex with Smallpox Inhibitor of Complement (SPICE)

PDB DOI: https://doi.org/10.2210/pdb5FOB/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens, Variola major virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-18 Released: 2016-04-06
Deposition Author(s): Forneris, F., Wu, J., Xue, X., Gros, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.230
R-Value Work: 0.198
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 206.81 kDa
Atom Count: 14,474
Modelled Residue Count: 1,784
Deposited Residue Count: 1,805
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT C3 BETA CHAIN	A	645	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024 Go to UniProtKB: P01024
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01024
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT C3B ALPHA' CHAIN	B	915	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024 Go to UniProtKB: P01024
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01024
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SMALLPOX INHIBITOR OF COMPLEMENT SPICE, D15L	C	245	Variola major virus	Mutation(s): 0
UniProt
Find proteins for Q76U65 (Variola virus) Explore Q76U65 Go to UniProtKB: Q76U65
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q76U65
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain LA [auth B] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain KA [auth B] SDF format, chain R [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain R [auth A]	IA [auth B] JA [auth B] KA [auth B] LA [auth B] R [auth A] IA [auth B], JA [auth B], KA [auth B], LA [auth B], R [auth A], S [auth A], T [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain BA [auth B] SDF format, chain EA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GA [auth B] SDF format, chain MA [auth B] SDF format, chain PA [auth C] SDF format, chain QA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C]	F [auth A], GA [auth B], MA [auth B], PA [auth C], QA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain GA [auth B] Focus chain MA [auth B] Focus chain PA [auth C] Focus chain QA [auth C] Interactions & Density Focus chain F [auth A] Focus chain GA [auth B] Focus chain MA [auth B] Focus chain PA [auth C] Focus chain QA [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain Q [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain Q [auth A]	HA [auth B], Q [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain HA [auth B] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.230
R-Value Work: 0.198
R-Value Observed: 0.199
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.891	α = 75.03
b = 83.311	β = 76.2
c = 127.377	γ = 68.5

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-06
Type: Initial release
Version 1.1: 2016-06-01
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary