Macromolecule Content

Total Structure Weight: 37.59 kDa
Atom Count: 2,346
Modelled Residue Count: 277
Deposited Residue Count: 327
Unique protein chains: 2

5N51

Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 3,4-Dibromothiophene-2-carboxylic acid

PDB DOI: 10.2210/pdb5N51/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-02-11 Released: 2018-02-28
Deposition Author(s): Siefker, C., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.207
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A crystallographic fragment study with human Pim-1 kinase

Siefker, C., Heine, A., Hardes, K., Steinmetzer, A., Klebe, G.

To be published.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	313	Homo sapiens	Mutation(s): 1 Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309 Go to UniProtKB: P11309
PHAROS: P11309
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11309
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pimtide	B	14	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8N8 Query on 8N8 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	3,4-bis(bromanyl)thiophene-2-carboxylic acid C₅ H₂ Br₂ O₂ S VMFBMYZXQCTXAV-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.207
R-Value Work: 0.181
R-Value Observed: 0.182
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.995	α = 90
b = 97.995	β = 90
c = 80.275	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2019-08-14
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.