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.

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
Sequence Annotations Expand
Reference Sequence

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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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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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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]	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]	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]	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]	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 J [auth L] SDF format, chain K [auth L] SDF format, chain L SDF format, chain I [auth L] SDF format, chain M [auth L] SDF format, chain N [auth L] SDF format, chain P [auth H] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain I [auth L] MOL2 format, chain M [auth L] MOL2 format, chain N [auth L] MOL2 format, chain P [auth H]	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]	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

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Deposit Data

Help and Resources

1DAN

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

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: 8

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)