2ZP0 | pdb_00002zp0

Human factor viia-tissue factor complexed with benzylsulfonamide-D-ile-gln-P-aminobenzamidine

PDB DOI: https://doi.org/10.2210/pdb2ZP0/pdb

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

Deposited: 2008-06-20 Released: 2008-07-15
Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.306 (Depositor), 0.272 (DCC)
R-Value Work:
0.218 (Depositor), 0.197 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Peptide Mimetic Factor VIIa Inhibitor: Importance of Hydrophilic Pocket in S2 Site to Improve Selectivity aganist Thrombin

Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Esaki, T., Sato, H., Watanabe, S., Itoh, S., Ohta, M., Kozono, T.

(2005) Lett Drug Des Discov 2: 177-181

Macromolecule Content

Total Structure Weight: 71.54 kDa
Atom Count: 5,032
Modeled Residue Count: 587
Deposited Residue Count: 624
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor VII light chain	A [auth L]	152	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor VII heavy chain	B [auth H]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	218	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13726
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PI0 Query on PI0 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]	(2S)-N-[(4-carbamimidoylphenyl)methyl]-2-[[(2R,3R)-3-methyl-2-(phenylmethylsulfonylamino)pentanoyl]amino]pentanediamide C₂₆ H₃₆ N₆ O₅ S RKXCEYZSZWJMTQ-FRGLQRNOSA-N		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 D [auth L] MOL2 format, chain D [auth L] mmCIF format, chain D [auth L]	D [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-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] mmCIF 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]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain N [auth H] SDF format, chain K [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain N [auth H] MOL2 format, chain K [auth L] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain N [auth H] mmCIF format, chain K [auth L]	F [auth L] G [auth L] H [auth L] I [auth L] J [auth L] F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth L] 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 H] Interactions & Density Focus chain F [auth L] 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 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.306 (Depositor), 0.272 (DCC)
R-Value Work: 0.218 (Depositor), 0.197 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.37	α = 90
b = 81.99	β = 90
c = 123.31	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2023-11-15
Changes: Data collection

2ZP0 | pdb_00002zp0

Human factor viia-tissue factor complexed with benzylsulfonamide-D-ile-gln-P-aminobenzamidine

Literature

Peptide Mimetic Factor VIIa Inhibitor: Importance of Hydrophilic Pocket in S2 Site to Improve Selectivity aganist Thrombin

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)