7KBT | pdb_00007kbt

Factor VIII in complex with the anti-C2 domain antibody, G99

PDB DOI: https://doi.org/10.2210/pdb7KBT/pdb

Classification: BLOOD CLOTTING/Immune System
Organism(s): Sus scrofa, Homo sapiens, Mus musculus
Expression System: Cricetulus griseus, Mus musculus
Mutation(s): No

Deposited: 2020-10-02 Released: 2020-11-18
Deposition Author(s): Ronayne, E.K., Gish, J., Wilson, C., Peters, S., Spencer, H.T., Spiegel, P.C., Childers, K.C.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.15 Å
R-Value Free:
0.338 (Depositor), 0.340 (DCC)
R-Value Work:
0.300 (Depositor), 0.300 (DCC)
R-Value Observed:
0.302 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of Blood Coagulation Factor VIII in Complex With an Anti-C2 Domain Non-Classical, Pathogenic Antibody Inhibitor

Ronayne, E.K., Peters, S.C., Gish, J.S., Wilson, C., Spencer, H.T., Doering, C.B., Lollar, P., Spiegel, P.C., Childers, K.C.

(2021) Front Immunol 12: 2260

DOI: https://doi.org/10.3389/fimmu.2021.697602

Macromolecule Content

Total Structure Weight: 217.12 kDa
Atom Count: 11,366
Modeled Residue Count: 1,444
Deposited Residue Count: 1,905
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII	A	1,467	Sus scrofa, Homo sapiens	Mutation(s): 0 Gene Names: F8, CF8, F8C
UniProt & NIH Common Fund Data Resources
Find proteins for P00451 (Homo sapiens) Explore P00451 Go to UniProtKB: P00451
PHAROS: P00451 GTEx: ENSG00000185010
Find proteins for P12263 (Sus scrofa) Explore P12263 Go to UniProtKB: P12263
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P12263P00451
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P00451-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G99 heavy chain	B [auth E]	224	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
G99 light chain	C [auth F]	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.15 Å
R-Value Free: 0.338 (Depositor), 0.340 (DCC)
R-Value Work: 0.300 (Depositor), 0.300 (DCC)
R-Value Observed: 0.302 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.243	α = 90
b = 132.243	β = 90
c = 380.029	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Adxv	data reduction
XDS	data reduction
PHASER	phasing
Aimless	data scaling
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MRI 1429164
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R15HL103518
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	U54HL141981
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R44HL117511
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R44HL110448
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	U54HL112309

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2021-06-16
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary