2BIL | pdb_00002bil

The human protein kinase Pim1 in complex with its consensus peptide Pimtide

PDB DOI: https://doi.org/10.2210/pdb2BIL/pdb

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

Deposited: 2005-01-22 Released: 2005-02-07
Deposition Author(s): Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.248 (Depositor), 0.251 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

The Human Protein Kinase Pim1 in Complex with its Consensus Peptide Pimtide

Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K.

To be published.

Macromolecule Content

Total Structure Weight: 37.64 kDa
Atom Count: 2,343
Modeled Residue Count: 281
Deposited Residue Count: 327
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CONSENSUS PIM1 PEPTIDE PIMTIDE	A	14	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1	B	313	Homo sapiens	Mutation(s): 1 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309 Go to UniProtKB: P11309
PHAROS: P11309 GTEx: ENSG00000137193
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11309
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BI1 Query on BI1 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3-YL}-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE C₂₅ H₂₄ N₄ O₂ QMGUOJYZJKLOLH-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.248 (Depositor), 0.251 (DCC)
R-Value Work: 0.192 (Depositor), 0.200 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.1	α = 90
b = 98.1	β = 90
c = 80.04	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-02-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-02-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2019-03-06
Changes: Data collection, Experimental preparation
Version 1.4: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.5: 2019-10-23
Changes: Data collection, Database references, Other
Version 1.6: 2023-12-13
Changes: Data collection, Database references, Refinement description