1DAN

Complex of active site inhibited human blood coagulation factor VIIA with human recombinant soluble tissue factor

PDB DOI: https://doi.org/10.2210/pdb1DAN/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Mesocricetus auratus, Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 1997-03-05 Released: 1997-09-04
Deposition Author(s): Banner, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.187
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor.

Banner, D.W., D'Arcy, A., Chene, C., Winkler, F.K., Guha, A., Konigsberg, W.H., Nemerson, Y., Kirchhofer, D.

(1996) Nature 380: 41-46

PubMed: 8598903 Search on PubMed
DOI: https://doi.org/10.1038/380041a0
Primary Citation of Related Structures:
1DAN

PubMed Abstract:
Blood coagulation is initiated when tissue factor binds to coagulation factor VIIa to give an enzymatically active complex which then activates factors IX and X, leading to thrombin generation and clot formation. We have determined the crystal structure at 2.0-A degrees resolution of active-site-inhibited factor VIIa complexed with the cleaved extracellular domain of tissue factor. In the complex, factor VIIa adopts an extended conformation. This structure provides a basis for understanding many molecular aspects of the initiation of coagulation.

Organizational Affiliation

Pharma Division, F. Hoffmann-La Roche, Basle, Switzerland.

Macromolecule Content

Total Structure Weight: 70 kDa
Atom Count: 4,971
Modelled Residue Count: 587
Deposited Residue Count: 607
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA light chain	A [auth L]	152	Homo sapiens	Mutation(s): 0 EC: 3.4.21.21 Membrane Entity: Yes
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
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth L]	Go to GlyGen: P08709-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BLOOD COAGULATION FACTOR VIIA heavy chain	B [auth H]	254	Homo sapiens	Mutation(s): 0 EC: 3.4.21.21 Membrane Entity: Yes
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
SOLUBLE TISSUE FACTOR	C [auth T]	80	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
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
SOLUBLE TISSUE FACTOR	D [auth U]	121	Homo sapiens	Mutation(s): 0 Membrane Entity: Yes
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0Z6 Query on 0Z6 Download Ideal Coordinates CCD File SDF format, chain O [auth H] MOL2 format, chain O [auth H] mmCIF format, chain O [auth H]	O [auth H]	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide C₂₅ H₃₆ Cl N₆ O₃ ZKHBINZTIMXMQW-CLAROIROSA-O		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain E [auth L] MOL2 format, chain E [auth L] mmCIF format, chain E [auth L]	E [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain E [auth L] Interactions & Density Focus chain E [auth L]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain F [auth L] MOL2 format, chain F [auth L] mmCIF format, chain F [auth L]	F [auth L]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain F [auth L] Interactions & Density Focus chain F [auth L]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain Q [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain Q [auth H]	Q [auth H]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain Q [auth H] Interactions & Density Focus chain Q [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain L SDF format, chain P [auth H] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain M [auth L] SDF format, chain N [auth L] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain L MOL2 format, chain P [auth H] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain M [auth L] MOL2 format, chain N [auth L] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain L mmCIF format, chain P [auth H] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain M [auth L] mmCIF format, chain N [auth L]	G [auth L] H [auth L] I [auth L] J [auth L] K [auth L] G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth L], P [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain P [auth H] Interactions & Density Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain P [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth H] MOL2 format, chain R [auth H] mmCIF format, chain R [auth H]	R [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth H] Interactions & Density Focus chain R [auth H]

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000369 (0Z6) Query on PRD_000369	O [auth H]	D-Phe-Phe-Arg Chloromethylketone	Peptide-like / Inhibitor		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.187
R-Value Observed: 0.187
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.65	α = 90
b = 82.55	β = 90
c = 126.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1997-09-04

Deposition Author(s):

Banner, D.W.

Revision History (Full details and data files)

Version 1.0: 1997-09-04
Type: Initial release
Version 1.1: 2008-03-10
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2012-12-12
Changes: Other
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary