BMRB: 18908

Human programmed cell death 1 receptor

Authors

Veverka, V., Cheng, X., Waters, L.C., Muskett, F.W., Morgan, S., Lesley, A., Griffiths, M., Stubberfield, C., Griffin, R., Henry, A.J., Robinson, M.K., Jansson, A., Ladbury, J.E., Ikemizu, S., Davis, S.J., Carr, M.D.

Assembly

Human programmed cell death 1 receptor

Entity

1. Human programmed cell death 1 receptor (polymer, Thiol state: all disulfide bound), 118 monomers, 13229.67 Da Detail

MPPTFSPALL VVTEGDNATF TCSFSNTSES FVLNWYRMSP SNQTDKLAAF PEDRSQPGQD SRFRVTQLPN GRDFHMSVVR ARRNDSGTYL CGAISLAPKA QIKESLRAEL RVTERRAE

Formula weight

13229.67 Da

Entity Connection

disulfide 1 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS22:SG	1:CYS91:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.3 %, Completeness: 91.8 %, Completeness (bb): 97.7 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	91.8 % (1238 of 1349)	93.6 % (660 of 705)	87.9 % (459 of 522)	97.5 % (119 of 122)
Backbone	97.7 % (676 of 692)	98.7 % (230 of 233)	96.6 % (337 of 349)	99.1 % (109 of 110)
Sidechain	87.4 % (673 of 770)	91.1 % (430 of 472)	81.5 % (233 of 286)	83.3 % (10 of 12)
Aromatic	39.2 % (40 of 102)	68.6 % (35 of 51)	8.0 % (4 of 50)	100.0 % (1 of 1)
Methyl	95.5 % (105 of 110)	96.4 % (53 of 55)	94.5 % (52 of 55)

1. Human programmed cell death 1 receptor

MPPTFSPALL VVTEGDNATF TCSFSNTSES FVLNWYRMSP SNQTDKLAAF PEDRSQPGQD SRFRVTQLPN GRDFHMSVVR ARRNDSGTYL CGAISLAPKA QIKESLRAEL RVTERRAE

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.4

#	Name	Isotope labeling	Type	Concentration
1	HPCD1R	[U-15N]		0.5 mM
2	potassium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		100 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.4

#	Name	Isotope labeling	Type	Concentration
6	HPCD1R	[U-13C; U-15N]		0.5 mM
7	potassium phosphate	natural abundance		25 mM
8	sodium chloride	natural abundance		100 mM
9	H2O	natural abundance		95 %
10	D2O	natural abundance		5 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.4

#	Name	Isotope labeling	Type	Concentration
11	HPCD1R	natural abundance		0.5 mM
12	potassium phosphate	natural abundance		25 mM
13	sodium chloride	natural abundance		100 mM
14	D2O	natural abundance		100 %

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LACS Plot; CA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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LACS Plot; CB

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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LACS Plot; CO

Referencing offset: 0.77 ppm, Outliers: 2 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

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Protein Blocks Logo

Calculated from 35 models in PDB: 2M2D, Strand ID: A Detail

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Release date

2013-02-20

Citation

Structure and interactions of the human programmed cell death 1 receptor
Cheng, X., Veverka, V., Radhakrishnan, A., Waters, L.C., Muskett, F.W., Morgan, S.H., Huo, J., Yu, C., Evans, E.J., Leslie, A.J., Griffiths, M., Stubberfield, C., Griffin, R., Henry, A.J., Jansson, A., Ladbury, J.E., Ikemizu, S., Carr, M.D., Davis, S.J.
J. Biol. Chem. (2013), 288, 11771-11785, PubMed 23417675 , DOI 10.1074/jbc.M112.448126 , Abstract

Related entities 1. Human programmed cell death 1 receptor, : 1 : 28 : 68 entities Detail

Interaction partners 1. Human programmed cell death 1 receptor, : 5 interactors Detail

Experiments performed 11 experiments Detail