2C4F

crystal structure of factor VII.stf complexed with pd0297121

PDB DOI: https://doi.org/10.2210/pdb2C4F/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2005-10-18 Released: 2006-10-18
Deposition Author(s): Kohrt, J.T., Zhang, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Work: 0.229
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 67.88 kDa
Atom Count: 5,058
Modelled Residue Count: 584
Deposited Residue Count: 587
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR VII PRECURSOR	A [auth H]	254	Homo sapiens	Mutation(s): 0 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR VII PRECURSOR	B [auth L]	142	Homo sapiens	Mutation(s): 0 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE FACTOR PRECURSOR	C [auth T]	75	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: P13726
PHAROS: P13726 GTEx: ENSG00000117525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE FACTOR PRECURSOR	D [auth U]	116	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726 Go to UniProtKB: P13726
PHAROS: P13726 GTEx: ENSG00000117525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GIL Query on GIL Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H]	F [auth H]	2-{[6-{3-[AMINO(IMINO)METHYL]PHENOXY}-4-(DIISOPROPYLAMINO)-3,5-DIFLUOROPYRIDIN-2-YL]OXY}-5-[(ISOBUTYLAMINO)CARBONYL]BEN ZOIC ACID C₃₀ H₃₅ F₂ N₅ O₅ JLWMMYZWEHHTFF-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth U] MOL2 format, chain M [auth U]	M [auth U]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth U] Interactions & Density Focus chain M [auth U]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain H [auth L] MOL2 format, chain H [auth L]	H [auth L]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain H [auth L] Interactions & Density Focus chain H [auth L]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L]	I [auth L]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain J [auth L] SDF format, chain L SDF format, chain E [auth H] SDF format, chain K [auth L] MOL2 format, chain G [auth L] MOL2 format, chain J [auth L] MOL2 format, chain L MOL2 format, chain E [auth H] MOL2 format, chain K [auth L]	E [auth H], G [auth L], J [auth L], K [auth L], L	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain G [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Interactions & Density Focus chain E [auth H] Focus chain G [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU Query on CGU	B [auth L]	L-PEPTIDE LINKING	C₆ H₉ N O₆		GLU

Binding Affinity Annotations
ID	Source	Binding Affinity
GIL	Binding MOAD: 2C4F	IC50: 20 (nM) from 1 assay(s)
	BindingDB: 2C4F	IC50: 20 (nM) from 1 assay(s)
	PDBBind: 2C4F	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Work: 0.229
R-Value Observed: 0.229
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.993	α = 90
b = 81.302	β = 90
c = 125.86	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-10-18

Deposition Author(s):

Kohrt, J.T.

Zhang, E.

Revision History (Full details and data files)

Version 1.0: 2006-10-18
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-07-12
Changes: Derived calculations
Version 1.4: 2019-05-22
Changes: Data collection, Refinement description
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary