BMRB Entry 4263

Name: dNumb PTB Domain Complexed with a Phosphotyrosine Peptide, NMR, Ensemble of Structures.
Published: 1999-10-05

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PDB ID: 2nmb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR4263
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

dNumb PTB Domain Complexed with a Phosphotyrosine Peptide, NMR, Ensemble of Structures.

Deposition date:

1998-10-30

Original release date:

1999-10-05

Authors:

Zwahlen, C.; Li, S.; Vincent, S.; Mcglade, C.; Kay, L.; Pawson, T.; Forman-Kay, J.

Citation:

Citation: Zwahlen, C.; Li, S.; Vincent, S.; Mcglade, C.; Kay, L.; Pawson, T.; Forman-Kay, J.. "Structure of a Numb PTB Domain-peptide Complex: A Basis for Diverse Binding Specificity" Nat. Struct. Biol. 5, 1075-1083 (1998).

Assembly members:

Assembly members:
PTB domain of Drosophila Numb protein, polymer, 160 residues, Formula weight is not available
GPpY peptide, polymer, 7 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Fruit Fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PTB domain of Drosophila Numb protein: GSPGIPDRVPESSKPHQWQA DEEAVRSATCSFSVKYLGCV EVFESRGMQVCEEALKVLRQ SRRRPVRGLLHVSGDGLRVV DDETKGLIVDQTIEKVSFCA PDRNHERGFSYICRDGTTRR WMCHGFLACKDSGERLSHAV GCAFAVCLERKQRRTRAAAS
GPpY peptide: AYIGPXL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shift_set_1
- assigned_chemical_shift_set_2

Data type	Count
13C chemical shifts	638
15N chemical shifts	171
1H chemical shifts	916

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	dNumb_PTB_one	1
2	GPpY_peptide_one	2
3	dNumb_PTB_two	1
4	GPpY_peptide_two	2

Entities:

Entity 1, dNumb_PTB_one 160 residues - Formula weight is not available

1	GLY	SER	PRO	GLY	ILE	PRO	ASP	ARG	VAL	PRO
2	GLU	SER	SER	LYS	PRO	HIS	GLN	TRP	GLN	ALA
3	ASP	GLU	GLU	ALA	VAL	ARG	SER	ALA	THR	CYS
4	SER	PHE	SER	VAL	LYS	TYR	LEU	GLY	CYS	VAL
5	GLU	VAL	PHE	GLU	SER	ARG	GLY	MET	GLN	VAL
6	CYS	GLU	GLU	ALA	LEU	LYS	VAL	LEU	ARG	GLN
7	SER	ARG	ARG	ARG	PRO	VAL	ARG	GLY	LEU	LEU
8	HIS	VAL	SER	GLY	ASP	GLY	LEU	ARG	VAL	VAL
9	ASP	ASP	GLU	THR	LYS	GLY	LEU	ILE	VAL	ASP
10	GLN	THR	ILE	GLU	LYS	VAL	SER	PHE	CYS	ALA
11	PRO	ASP	ARG	ASN	HIS	GLU	ARG	GLY	PHE	SER
12	TYR	ILE	CYS	ARG	ASP	GLY	THR	THR	ARG	ARG
13	TRP	MET	CYS	HIS	GLY	PHE	LEU	ALA	CYS	LYS
14	ASP	SER	GLY	GLU	ARG	LEU	SER	HIS	ALA	VAL
15	GLY	CYS	ALA	PHE	ALA	VAL	CYS	LEU	GLU	ARG
16	LYS	GLN	ARG	ARG	THR	ARG	ALA	ALA	ALA	SER

Entity 2, GPpY_peptide_one 7 residues - Formula weight is not available

1

ALA

TYR

ILE

GLY

PRO

PTR

LEU

Samples:

sample_1: PTB domain of Drosophila Numb protein, [U-100% 13C; U-100% 15N], 1.2 mM; GPpY peptide, [99% 12C; 99% 14N]-pY, ALA [100% 13C, 100% 15N]-TYR, ILE, GLY, PRO, LEU ,

sample_conditions_1: ionic strength: 0.22; pH: 6.0; pressure: 1 bar; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
not available	sample_1	not available	sample_conditions_1

Software:

NMRPipe - NMR data processing

NMRView - Data analysis, Peak picking, Semi-automated assignment

X-PLOR v3.158 - Structure calculation

ARIA - Structure calculation

NMR spectrometers:

Varian Unity Plus 500 MHz
Varian Inova 600 MHz

BMRB	4683
PDB	1DDM 2NMB
GB	AAA28730 AAF52776 AAK93152 AAN10693 ACL68752
REF	NP_001260291 NP_523523 NP_723460 XP_001357245 XP_001964877
SP	P16554
AlphaFold	P16554

1	GLY	SER	PRO	GLY	ILE	PRO	ASP	ARG	VAL	PRO
2	GLU	SER	SER	LYS	PRO	HIS	GLN	TRP	GLN	ALA
3	ASP	GLU	GLU	ALA	VAL	ARG	SER	ALA	THR	CYS
4	SER	PHE	SER	VAL	LYS	TYR	LEU	GLY	CYS	VAL
5	GLU	VAL	PHE	GLU	SER	ARG	GLY	MET	GLN	VAL
6	CYS	GLU	GLU	ALA	LEU	LYS	VAL	LEU	ARG	GLN
7	SER	ARG	ARG	ARG	PRO	VAL	ARG	GLY	LEU	LEU
8	HIS	VAL	SER	GLY	ASP	GLY	LEU	ARG	VAL	VAL
9	ASP	ASP	GLU	THR	LYS	GLY	LEU	ILE	VAL	ASP
10	GLN	THR	ILE	GLU	LYS	VAL	SER	PHE	CYS	ALA
11	PRO	ASP	ARG	ASN	HIS	GLU	ARG	GLY	PHE	SER
12	TYR	ILE	CYS	ARG	ASP	GLY	THR	THR	ARG	ARG
13	TRP	MET	CYS	HIS	GLY	PHE	LEU	ALA	CYS	LYS
14	ASP	SER	GLY	GLU	ARG	LEU	SER	HIS	ALA	VAL
15	GLY	CYS	ALA	PHE	ALA	VAL	CYS	LEU	GLU	ARG
16	LYS	GLN	ARG	ARG	THR	ARG	ALA	ALA	ALA	SER

1	GLY	SER	PRO	GLY	ILE	PRO	ASP	ARG	VAL	PRO
2	GLU	SER	SER	LYS	PRO	HIS	GLN	TRP	GLN	ALA
3	ASP	GLU	GLU	ALA	VAL	ARG	SER	ALA	THR	CYS
4	SER	PHE	SER	VAL	LYS	TYR	LEU	GLY	CYS	VAL
5	GLU	VAL	PHE	GLU	SER	ARG	GLY	MET	GLN	VAL
6	CYS	GLU	GLU	ALA	LEU	LYS	VAL	LEU	ARG	GLN
7	SER	ARG	ARG	ARG	PRO	VAL	ARG	GLY	LEU	LEU
8	HIS	VAL	SER	GLY	ASP	GLY	LEU	ARG	VAL	VAL
9	ASP	ASP	GLU	THR	LYS	GLY	LEU	ILE	VAL	ASP
10	GLN	THR	ILE	GLU	LYS	VAL	SER	PHE	CYS	ALA
11	PRO	ASP	ARG	ASN	HIS	GLU	ARG	GLY	PHE	SER
12	TYR	ILE	CYS	ARG	ASP	GLY	THR	THR	ARG	ARG
13	TRP	MET	CYS	HIS	GLY	PHE	LEU	ALA	CYS	LYS
14	ASP	SER	GLY	GLU	ARG	LEU	SER	HIS	ALA	VAL
15	GLY	CYS	ALA	PHE	ALA	VAL	CYS	LEU	GLU	ARG
16	LYS	GLN	ARG	ARG	THR	ARG	ALA	ALA	ALA	SER