3OP0 | pdb_00003op0

Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide

PDB DOI: https://doi.org/10.2210/pdb3OP0/pdb

Classification: SIGNALING PROTEIN/SIGNALING PROTEIN REGULATOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-08-31 Released: 2010-10-20
Deposition Author(s): Chaikuad, A., Guo, K., Cooper, C.D.O., Ayinampudi, V., Krojer, T., Ugochukwu, E., Muniz, J.R.C., Vollmar, M., Canning, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.266 (Depositor), 0.258 (DCC)
R-Value Work:
0.214 (Depositor), 0.212 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide

Chaikuad, A., Guo, K., Cooper, C.D.O., Ayinampudi, V., Krojer, T., Ugochukwu, E., Muniz, J.R.C., Vollmar, M., Canning, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Bountra, C., Bullock, A.

To be published.

Macromolecule Content

Total Structure Weight: 75.08 kDa
Atom Count: 5,481
Modeled Residue Count: 662
Deposited Residue Count: 668
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal transduction protein CBL-C	A, B	323	Homo sapiens	Mutation(s): 1 Gene Names: CBL3, CBLC, RNF57 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULV8 (Homo sapiens) Explore Q9ULV8 Go to UniProtKB: Q9ULV8
PHAROS: Q9ULV8 GTEx: ENSG00000142273
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ULV8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	C, D	11	Homo sapiens	Mutation(s): 0 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533 Go to UniProtKB: P00533
PHAROS: P00533 GTEx: ENSG00000146648
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS
CSO Query on CSO	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
PTR Query on PTR	C, D	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.266 (Depositor), 0.258 (DCC)
R-Value Work: 0.214 (Depositor), 0.212 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.25	α = 90
b = 90.25	β = 90
c = 191.581	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-06
Changes: Structure summary