5MHM | pdb_00005mhm

FXIIIa in complex with the inhibitor ZED1630

PDB DOI: https://doi.org/10.2210/pdb5MHM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2016-11-24 Released: 2017-12-20
Deposition Author(s): Stieler, M., Heine, A., Klebe, G.
Funding Organization(s): BMBF

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

FXIIIa in complex with the inhibitor Mi0621

Stieler, M., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 171.63 kDa
Atom Count: 11,759
Modeled Residue Count: 1,383
Deposited Residue Count: 1,492
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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: F13A1, F13A 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
inhibitor ZED1630	C [auth H], D [auth O]	8	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], T [auth B], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] Q [auth B] H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [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 Q [auth B] Focus chain R [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 Q [auth B] Focus chain R [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] O [auth B] P [auth B] E [auth A], F [auth A], G [auth A], O [auth B], P [auth B], S [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 O [auth B] Focus chain P [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain L [auth A] MOL2 format, chain W [auth B] MOL2 format, chain L [auth A] mmCIF format, chain W [auth B] mmCIF format, chain L [auth A]	L [auth A], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain W [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE Query on NLE	C [auth H], D [auth O]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.912	α = 88.44
b = 80.715	β = 76.6
c = 103.19	γ = 81.79

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Stieler, M.

Heine, A.

Klebe, G.

Funding Organization	Location	Grant Number
BMBF	Germany	FKZ0316030

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy
Version 2.1: 2024-11-20
Changes: Structure summary