4ZMA

Crystal Structure of a FVIIa-Trypsin Chimera (ST) in Complex with Soluble Tissue Factor

PDB DOI: https://doi.org/10.2210/pdb4ZMA/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-05-02 Released: 2015-12-30
Deposition Author(s): Sorensen, A.B., Svensson, L.A., Gandhi, P.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.295
R-Value Work: 0.240
R-Value Observed: 0.243

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 71.21 kDa
Atom Count: 4,834
Modelled Residue Count: 586
Deposited Residue Count: 620
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
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	B [auth H]	249	Homo sapiens	Mutation(s): 6 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	219	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0Z6 Query on 0Z6 Download Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H]	M [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 M [auth H] Interactions & Density Focus chain M [auth H]
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain K [auth L] MOL2 format, chain K [auth L]	K [auth L]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain K [auth L] Interactions & Density Focus chain K [auth L]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain L MOL2 format, chain L	L	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain L Interactions & Density Focus chain L
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain O [auth H]	O [auth H], P [auth H]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain O [auth H] Focus chain P [auth H] Interactions & Density Focus chain O [auth H] Focus chain P [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain D [auth L] SDF format, chain G [auth L] SDF format, chain N [auth H] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain D [auth L] MOL2 format, chain G [auth L] MOL2 format, chain N [auth H]	D [auth L] E [auth L] F [auth L] G [auth L] H [auth L] D [auth L], E [auth L], F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], N [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain E [auth L] 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 N [auth H] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] 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 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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000369 (0Z6) Query on PRD_000369	M [auth H]	D-Phe-Phe-Arg Chloromethylketone	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: 2.30 Å
R-Value Free: 0.295
R-Value Work: 0.240
R-Value Observed: 0.243
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.209	α = 90
b = 80.898	β = 90
c = 125.759	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-30

Deposition Author(s):

Sorensen, A.B.

Svensson, L.A.

Gandhi, P.S.

Revision History (Full details and data files)

Version 1.0: 2015-12-30
Type: Initial release
Version 1.1: 2016-01-13
Changes: Database references
Version 1.2: 2016-03-09
Changes: Database references
Version 1.3: 2016-12-21
Changes: Non-polymer description
Version 1.4: 2018-01-17
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

4ZMA

Crystal Structure of a FVIIa-Trypsin Chimera (ST) in Complex with Soluble Tissue Factor

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

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: 7

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)