BMRB Entry 18908

Name: Human programmed cell death 1 receptor
Published: 2013-02-21

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PDB ID: 2m2d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18908
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Human programmed cell death 1 receptor

Deposition date:

2012-12-18

Original release date:

2013-02-21

Authors:

Veverka, Vaclav; Cheng, Xiaoxiao; Waters, Lorna; Muskett, Frederick; Morgan, Sara; Lesley, Alastair; Griffiths, Merryn; Stubberfield, Colin; Griffin, Robert; Henry, Alistair; Robinson, Martyn; Jansson, Andreas; Ladbury, John; Ikemizu, Shinji; Davis, Simon; Carr, Mark

Citation:

Citation: Cheng, Xiaoxiao; Veverka, Vaclav; Radhakrishnan, Anand; Waters, Lorna; Muskett, Frederick; Morgan, Sara; Huo, Jiandong; Yu, Chao; Evans, Edward; Leslie, Alasdair; Griffiths, Meryn; Stubberfield, Colin; Griffin, Robert; Henry, Alistair; Jansson, Andreas; Ladbury, John; Ikemizu, Shinji; Carr, Mark; Davis, Simon. "Structure and interactions of the human programmed cell death 1 receptor." J. Biol. Chem. 288, 11771-11785 (2013).
PubMed: 23417675

Assembly members:

Assembly members:
Human programmed cell death 1 receptor, polymer, 118 residues, 13245.914 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Human programmed cell death 1 receptor: MPPTFSPALLVVTEGDNATF TCSFSNTSESFVLNWYRMSP SNQTDKLAAFPEDRSQPGQD SRFRVTQLPNGRDFHMSVVR ARRNDSGTYLCGAISLAPKA QIKESLRAELRVTERRAE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	453
15N chemical shifts	119
1H chemical shifts	774

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Human programmed cell death 1 receptor	1

Entities:

Entity 1, Human programmed cell death 1 receptor 118 residues - 13245.914 Da.

1

MET

PRO

THR

PHE

SER

PRO

ALA

LEU

2

VAL

THR

GLU

GLY

ASP

ASN

ALA

THR

PHE

3

THR

CYS

SER

PHE

SER

ASN

THR

SER

GLU

SER

4

PHE

VAL

LEU

ASN

TRP

TYR

ARG

MET

SER

PRO

5

SER

ASN

GLN

THR

ASP

LYS

LEU

ALA

PHE

6

PRO

GLU

ASP

ARG

SER

GLN

PRO

GLY

GLN

ASP

7

SER

ARG

PHE

ARG

VAL

THR

GLN

LEU

PRO

ASN

8

GLY

ARG

ASP

PHE

HIS

MET

SER

VAL

ARG

9

ALA

ARG

ASN

ASP

SER

GLY

THR

TYR

LEU

10

CYS

GLY

ALA

ILE

SER

LEU

ALA

PRO

LYS

ALA

11

GLN

ILE

LYS

GLU

SER

LEU

ARG

ALA

GLU

LEU

12

ARG

VAL

THR

GLU

ARG

ALA

GLU

Samples:

sample_N: HPCD1R, [U-15N], 0.5 mM; potassium phosphate 25 mM; sodium chloride 100 mM; H2O 95%; D2O 5%

sample_CN: HPCD1R, [U-13C; U-15N], 0.5 mM; potassium phosphate 25 mM; sodium chloride 100 mM; H2O 95%; D2O 5%

sample_AR: HPCD1R 0.5 mM; potassium phosphate 25 mM; sodium chloride 100 mM; D2O 100%

sample_conditions_1: ionic strength: 0.125 M; pH: 6.4; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_N	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_CN	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_AR	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_AR	isotropic	sample_conditions_1
3D HNCACB	sample_CN	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_CN	isotropic	sample_conditions_1
3D HNCO	sample_CN	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_CN	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_N	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_CN	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_N	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

SPARKY, Goddard - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

PDB	2M2D 3RRQ 4ZQK
DBJ	BAG36577 BAJ21104
GB	AAC41700 AAC51773 AAH74740 AAN64003 AAO25116
REF	NP_005009 XP_003776178 XP_004033550 XP_006712636 XP_006725049
SP	Q15116
AlphaFold	Q15116