1J9C | pdb_00001j9c

Crystal Structure of tissue factor-factor VIIa complex

PDB DOI: https://doi.org/10.2210/pdb1J9C/pdb

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

Deposited: 2001-05-24 Released: 2004-07-27
Deposition Author(s): Huang, M., Ruf, W., Edgington, T.S., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.299 (Depositor)
R-Value Work:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Ligand Induced Conformational Transitions of Tissue Factor. Crystal Structure of the Tissue Factor:Factor VIIa Complex.

Huang, M., Ruf, W., Edgington, T.S., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 63.35 kDa
Atom Count: 4,559
Modeled Residue Count: 559
Deposited Residue Count: 559
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	A [auth T]	210	Homo sapiens	Mutation(s): 0
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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
factor VIIa light chain	B [auth L]	95	Homo sapiens	Mutation(s): 0 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: 1	Glycosylation Focus chain B [auth L]	Go to GlyGen: P08709-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
factor VIIa heavy chain	C [auth H]	254	Homo sapiens	Mutation(s): 0 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: 1	Glycosylation Focus chain C [auth H]	Go to GlyGen: P08709-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0Z6 Query on 0Z6 Download:Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [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 F [auth H]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth H]
GLC Query on GLC 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]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain D [auth L]
FUL Query on FUL 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-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-KGJVWPDLSA-N		Interactions Focus chain E [auth L]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H mmCIF format, chain H	H	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000369 (0Z6) Query on PRD_000369	F [auth H]	D-Phe-Phe-Arg Chloromethylketone	Peptide-like / Inhibitor		Interactions Focus chain F [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.299 (Depositor)
R-Value Work: 0.221 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.038	α = 90
b = 68.302	β = 92.12
c = 78.438	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-27
Type: Initial release
Version 1.1: 2008-04-27
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: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-10-30
Changes: Structure summary