4KTY | pdb_00004kty

Fibrin-stabilizing factor with a bound ligand

PDB DOI: https://doi.org/10.2210/pdb4KTY/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2013-05-21 Released: 2013-12-04
Deposition Author(s): Stieler, M., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.206 (Depositor), 0.207 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants.

Stieler, M., Weber, J., Hils, M., Kolb, P., Heine, A., Buchold, C., Pasternack, R., Klebe, G.

(2013) Angew Chem Int Ed Engl 52: 11930-11934

PubMed: 24115223 Search on PubMed
DOI: https://doi.org/10.1002/anie.201305133
Primary Citation Related Structures:
4KTY

Organizational Affiliation

Department of Pharmaceutical Chemistry, Philipps-University, Marbacher Weg 6, 35032 Marburg (Germany).

Macromolecule Content

Total Structure Weight: 171.65 kDa
Atom Count: 12,087
Modeled Residue Count: 1,411
Deposited Residue Count: 1,494
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XIII A chain	A, B	738	Homo sapiens	Mutation(s): 2 Gene Names: F13A, F13A1 EC: 2.3.2.13
UniProt & NIH Common Fund Data Resources
Find proteins for P00488 (Homo sapiens) Explore P00488 Go to UniProtKB: P00488
PHAROS: P00488 GTEx: ENSG00000124491
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00488
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide-like ligand	C, D	9	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	E [auth A] F [auth A] G [auth A] N [auth B] O [auth B] E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
1TX Query on 1TX	C, D	L-PEPTIDE LINKING	C₈ H₁₅ N O₄		--
ABA Query on ABA	C, D	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
DAS Query on DAS	C, D	D-PEPTIDE LINKING	C₄ H₇ N O₄		--
NLE Query on NLE	C, D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001125 Query on PRD_001125	C, D	N-[(2S)-2-({(2S)-2-[(N-acetyl-D-alpha-aspartyl)amino]-7-methoxy-7-oxoheptanoyl}amino)butanoyl]-L-norleucyl-L-leucyl-L-prolyl-L-tryptophyl-L-proline	Peptide-like / Inhibitor		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.206 (Depositor), 0.207 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.761	α = 88.14
b = 80.51	β = 76.7
c = 102.844	γ = 82.01

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-12-04

Deposition Author(s):

Stieler, M.

Heine, A.

Klebe, G.

Revision History (Full details and data files)

Version 1.0: 2013-12-04
Type: Initial release
Version 1.1: 2014-03-12
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations

4KTY | pdb_00004kty

Fibrin-stabilizing factor with a bound ligand

Literature

Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2