4IBL | pdb_00004ibl

Rubidium Sites in Blood Coagulation Factor VIIa

PDB DOI: https://doi.org/10.2210/pdb4IBL/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2012-12-08 Released: 2014-04-16
Deposition Author(s): Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Bajaj, S.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.175 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

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

Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium

Vadivel, K., Schmidt, A., Cascio, D., Padmanabhan, K., Krishnaswamy, S., Brandstetter, H., Bajaj, S.P.

(2021) Acta Crystallogr D Biol Crystallogr D77: 809-819

DOI: https://doi.org/10.1107/S2059798321003922

Macromolecule Content

Total Structure Weight: 71.77 kDa
Atom Count: 5,267
Modeled Residue Count: 592
Deposited Residue Count: 625
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	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: 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
Coagulation factor VII	B [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
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]	219	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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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]
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain P [auth H] MOL2 format, chain P [auth H] mmCIF format, chain P [auth H]	P [auth H]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain P [auth H] Interactions & Density Focus chain P [auth H]
RB Query on RB Download:Ideal Coordinates CCD File SDF format, chain N [auth L] SDF format, chain T [auth H] SDF format, chain S [auth H] SDF format, chain O [auth L] SDF format, chain J [auth L] SDF format, chain H [auth L] MOL2 format, chain N [auth L] MOL2 format, chain T [auth H] MOL2 format, chain S [auth H] MOL2 format, chain O [auth L] MOL2 format, chain J [auth L] MOL2 format, chain H [auth L] mmCIF format, chain N [auth L] mmCIF format, chain T [auth H] mmCIF format, chain S [auth H] mmCIF format, chain O [auth L] mmCIF format, chain J [auth L] mmCIF format, chain H [auth L]	H [auth L] J [auth L] N [auth L] O [auth L] S [auth H] H [auth L], J [auth L], N [auth L], O [auth L], S [auth H], T [auth H]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain J [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain S [auth H] Focus chain T [auth H] Interactions & Density Focus chain H [auth L] Focus chain J [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain S [auth H] Focus chain T [auth H]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth L] SDF format, chain M [auth L] SDF format, chain Q [auth H] SDF format, chain G [auth L] MOL2 format, chain K [auth L] MOL2 format, chain M [auth L] MOL2 format, chain Q [auth H] MOL2 format, chain G [auth L] mmCIF format, chain K [auth L] mmCIF format, chain M [auth L] mmCIF format, chain Q [auth H] mmCIF format, chain G [auth L]	G [auth L], K [auth L], M [auth L], Q [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Focus chain K [auth L] Focus chain M [auth L] Focus chain Q [auth H] Interactions & Density Focus chain G [auth L] Focus chain K [auth L] Focus chain M [auth L] Focus chain Q [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth H] SDF format, chain U [auth H] SDF format, chain W [auth T] SDF format, chain V [auth H] MOL2 format, chain R [auth H] MOL2 format, chain U [auth H] MOL2 format, chain W [auth T] MOL2 format, chain V [auth H] mmCIF format, chain R [auth H] mmCIF format, chain U [auth H] mmCIF format, chain W [auth T] mmCIF format, chain V [auth H]	R [auth H], U [auth H], V [auth H], W [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain R [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth T] Interactions & Density Focus chain R [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth T]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain L SDF format, chain I [auth L] MOL2 format, chain F [auth L] MOL2 format, chain L MOL2 format, chain I [auth L] mmCIF format, chain F [auth L] mmCIF format, chain L mmCIF format, chain I [auth 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

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: 1.80 Å
R-Value Free: 0.215 (Depositor), 0.216 (DCC)
R-Value Work: 0.175 (Depositor), 0.179 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.9	α = 90
b = 81.06	β = 90
c = 126.42	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-16
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2021-06-09
Changes: Database references, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection