6DCM | pdb_00006dcm

The atomic resolution crystal structure of Kringle 2 variant bound with EACA

PDB DOI: https://doi.org/10.2210/pdb6DCM/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2018-05-07 Released: 2019-05-15
Deposition Author(s): Ghanbarpour, A., Geiger, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free:
0.157 (Depositor), 0.195 (DCC)
R-Value Work:
0.141 (Depositor)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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This is version 2.1 of the entry. See complete history.

Literature

The atomic resolution crystal structure of Kringle 2 variant bound with EACA

Ghanbarpour, A., Geiger, J.

To be published.

Macromolecule Content

Total Structure Weight: 9.93 kDa
Atom Count: 822
Modeled Residue Count: 85
Deposited Residue Count: 85
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen	A	85	Homo sapiens	Mutation(s): 0 Gene Names: PLG EC: 3.4.21.7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACA Query on ACA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-AMINOHEXANOIC ACID C₆ H₁₃ N O₂ SLXKOJJOQWFEFD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.157 (Depositor), 0.195 (DCC)
R-Value Work: 0.141 (Depositor)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.825	α = 90
b = 39.006	β = 110.36
c = 31.316	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Ghanbarpour, A.

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.