2B8O | pdb_00002b8o

Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/Soluble Tissue Factor Complex

PDB DOI: https://doi.org/10.2210/pdb2B8O/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2005-10-08 Released: 2007-02-13
Deposition Author(s): Bajaj, S.P., Schmidt, A.E., Padmanabhan, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.285 (Depositor), 0.344 (DCC)
R-Value Work:
0.225 (Depositor), 0.213 (DCC)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Factor VIIa/soluble Tissue Factor complexed with Glu-Gly-Arg-Chloromethyl ketone

Bajaj, S.P., Schmidt, A.E., Padmanabhan, K.

To be published.

Macromolecule Content

Total Structure Weight: 69.06 kDa
Atom Count: 4,959
Modeled 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
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth L]	Go to GlyGen: P08709-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation 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% 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
0GJ Query on 0GJ Download Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H] mmCIF format, chain M [auth H]	M [auth H]	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide C₁₄ H₂₈ Cl N₆ O₅ XELWNHKFCNMWQO-LPEHRKFASA-O		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [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] 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]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain Q [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain P [auth H] mmCIF format, chain Q [auth H]	P [auth H], Q [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth H] Focus chain Q [auth H] Interactions & Density Focus chain P [auth H] Focus chain Q [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain L SDF format, chain N [auth H] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain L MOL2 format, chain N [auth H] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain L mmCIF format, chain N [auth H]	F [auth L] G [auth L] I [auth L] J [auth L] L F [auth L], G [auth L], I [auth L], J [auth L], L, N [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain G [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain L Focus chain N [auth H] Interactions & Density Focus chain F [auth L] Focus chain G [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain L Focus chain N [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth H] SDF format, chain S [auth H] SDF format, chain T MOL2 format, chain R [auth H] MOL2 format, chain S [auth H] MOL2 format, chain T mmCIF format, chain R [auth H] mmCIF format, chain S [auth H] mmCIF format, chain T	R [auth H], S [auth H], T	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth H] Focus chain S [auth H] Focus chain T Interactions & Density Focus chain R [auth H] Focus chain S [auth H] Focus chain T
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain K [auth L] MOL2 format, chain H [auth L] MOL2 format, chain K [auth L] mmCIF format, chain H [auth L] mmCIF format, chain K [auth L]	H [auth L], K [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain K [auth L] Interactions & Density Focus chain H [auth L] Focus chain K [auth L]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth H] Interactions & Density Focus chain O [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_000288 (0GJ) Query on PRD_000288	M [auth H]	GLU-GLY-ARG-CHLOROMETHYL KETONE	Peptide-like / Inhibitor		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.285 (Depositor), 0.344 (DCC)
R-Value Work: 0.225 (Depositor), 0.213 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.28	α = 90
b = 81.11	β = 90
c = 126.86	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Bajaj, S.P.

Schmidt, A.E.

Padmanabhan, K.

Revision History (Full details and data files)

Version 1.0: 2007-02-13
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: Advisory, Data collection, Derived calculations, Structure summary
Version 1.5: 2025-03-26
Changes: Data collection, Database references, Structure summary

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Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor VIIa/Soluble Tissue Factor Complex

Crystal Structure of Factor VIIa/soluble Tissue Factor complexed with Glu-Gly-Arg-Chloromethyl ketone

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

Entity ID: 8

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

2B8O | pdb_00002b8o