3HRZ

Cobra Venom Factor (CVF) in complex with human factor B

PDB DOI: https://doi.org/10.2210/pdb3HRZ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Naja kaouthia, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2009-06-10 Released: 2009-07-07
Deposition Author(s): Janssen, B.J.C., Gomes, L., Koning, R.I., Svergun, D.I., Koster, A.J., Fritzinger, D.C., Vogel, C.-W., Gros, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.226
R-Value Work: 0.180
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 227.04 kDa
Atom Count: 15,938
Modelled Residue Count: 1,902
Deposited Residue Count: 1,999
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobra venom factor	A	627	Naja kaouthia	Mutation(s): 0
UniProt
Find proteins for Q91132 (Naja kaouthia) Explore Q91132 Go to UniProtKB: Q91132
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91132
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobra venom factor	B	252	Naja kaouthia	Mutation(s): 0
UniProt
Find proteins for Q91132 (Naja kaouthia) Explore Q91132 Go to UniProtKB: Q91132
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91132
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobra venom factor	C	379	Naja kaouthia	Mutation(s): 0
UniProt
Find proteins for Q91132 (Naja kaouthia) Explore Q91132 Go to UniProtKB: Q91132
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91132
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement factor B	D	741	Homo sapiens	Mutation(s): 2 Gene Names: CFB, BF, BFD EC: 3.4.21.47
UniProt & NIH Common Fund Data Resources
Find proteins for P00751 (Homo sapiens) Explore P00751 Go to UniProtKB: P00751
PHAROS: P00751 GTEx: ENSG00000243649
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00751
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C]	I [auth A], L [auth C]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Interactions & Density Focus chain I [auth A] Focus chain L [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	F [auth A], K [auth C], N [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth C] Focus chain N [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D]	J [auth B], M [auth C], P [auth D], Q [auth D], R [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth D]	G [auth A], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.226
R-Value Work: 0.180
R-Value Observed: 0.181
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.89	α = 90
b = 283.39	β = 90
c = 134.4	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2021-03-31
Changes: Source and taxonomy, Structure summary
Version 2.2: 2021-10-13
Changes: Database references
Version 2.3: 2023-09-06
Changes: Data collection, Refinement description

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Deposit Data

Help and Resources

3HRZ

Cobra Venom Factor (CVF) in complex with human factor B

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)