2FIR

Crystal structure of DFPR-VIIa/sTF

PDB DOI: https://doi.org/10.2210/pdb2FIR/pdb

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

Deposited: 2005-12-30 Released: 2006-07-11
Deposition Author(s): Bajaj, S.P., Schmidt, A.E., Padmanabhan, K., Bajaj, M.S., Prevost, D., Schreuder, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.281
R-Value Work: 0.207

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: 69.13 kDa
Atom Count: 5,352
Modelled Residue Count: 587
Deposited Residue Count: 601
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 VII Light chain	A [auth L]	142	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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII Heavy Chain (EC 3.4.21.21)	B [auth H]	254	Homo sapiens	Mutation(s): 0 Gene Names: F7
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	C [auth T]	205	Homo sapiens	Mutation(s): 0 Gene Names: F3
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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0G7 Query on 0G7 Download Ideal Coordinates CCD File SDF format, chain N [auth H] MOL2 format, chain N [auth H]	N [auth H]	D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide C₂₁ H₃₁ Cl N₆ O₃ KWPACVJPAFGBEQ-IKGGRYGDSA-N		Interactions Focus chain N [auth H] Interactions & Density Focus chain N [auth H]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L]	D [auth L]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain E [auth L] MOL2 format, chain E [auth L]	E [auth L]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain E [auth L] Interactions & Density Focus chain E [auth L]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Q [auth H] SDF format, chain R [auth H] MOL2 format, chain Q [auth H] MOL2 format, chain R [auth H]	Q [auth H], R [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth H] Focus chain R [auth H] Interactions & Density Focus chain Q [auth H] Focus chain R [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain M [auth L] 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 O [auth H] MOL2 format, chain M [auth L] 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 O [auth H]	G [auth L] H [auth L] J [auth L] K [auth L] M [auth L] G [auth L], H [auth L], J [auth L], K [auth L], M [auth L], O [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain M [auth L] Focus chain O [auth H] Interactions & Density Focus chain G [auth L] Focus chain H [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain M [auth L] Focus chain O [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain T [auth H] SDF format, chain U [auth T] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] MOL2 format, chain U [auth T]	S [auth H], T [auth H], U [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth T] Interactions & Density Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth T]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain I [auth L] SDF format, chain L MOL2 format, chain F [auth L] MOL2 format, chain I [auth L] MOL2 format, chain L	F [auth L], I [auth L], L	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain I [auth L] Focus chain L Interactions & Density Focus chain F [auth L] Focus chain I [auth L] Focus chain L
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain P [auth H] MOL2 format, chain P [auth H]	P [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth H] Interactions & Density Focus chain P [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_000021 (0G7) Query on PRD_000021	N [auth H]	D-Phe-Pro-Arg chloromethylketone (PPACK)	Peptide-like / Inhibitor		Interactions Focus chain N [auth H] Interactions & Density Focus chain N [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.281
R-Value Work: 0.207
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.02	α = 90
b = 80.98	β = 90
c = 126.33	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-07-11
Type: Initial release
Version 1.1: 2008-05-01
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: 2013-02-27
Changes: Other
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

2FIR

Crystal structure of DFPR-VIIa/sTF

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: 8

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)