5PB1

Crystal Structure of Factor VIIa in complex with benzenecarboximidamide

PDB DOI: https://doi.org/10.2210/pdb5PB1/pdb
Deposition Group: G_1002015 ExploreG_1002015

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-10 Released: 2017-06-21
Deposition Author(s): Stihle, M., Mayweg, A., Roever, S., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.210
R-Value Work: 0.190
R-Value Observed: 0.191

Starting Model: other
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Factor VIIa complex

Mayweg, A., Roever, S., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 36.21 kDa
Atom Count: 2,917
Modelled Residue Count: 306
Deposited Residue Count: 318
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII light chain	A	64	Homo sapiens	Mutation(s): 0 Gene Names: F7 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII heavy chain	B [auth D]	254	Homo sapiens	Mutation(s): 0 Gene Names: F7 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth D] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain N [auth D] MOL2 format, chain C [auth A] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain N [auth D] mmCIF format, chain C [auth A] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain N [auth D]	C [auth A] G [auth D] H [auth D] I [auth D] J [auth D] C [auth A], G [auth D], H [auth D], I [auth D], J [auth D], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain N [auth D] Interactions & Density Focus chain C [auth A] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	D [auth A], E [auth A], K [auth D], L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth D] Focus chain L [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHO Query on MHO	B [auth D]	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.210
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.676	α = 90
b = 95.676	β = 90
c = 117.961	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-06-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-06-21
Type: Initial release
Version 1.1: 2018-02-21
Changes: Structure summary
Version 2.0: 2021-08-18
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-11-17
Changes: Structure summary
Version 2.2: 2024-04-03
Changes: Data collection, Refinement description
Version 2.3: 2024-11-13
Changes: Structure summary

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Help and Resources

5PB1

Crystal Structure of Factor VIIa in complex with benzenecarboximidamide

Crystal Structure of a Factor VIIa complex

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2