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BMRB: 15189

2JOP

Solution structure of the N-terminal extracellular domain of the lymphocyte receptor CD5 (CD5 domain 1)

Authors

Garza-Garcia, A., Harris, R., Esposito, D., Driscoll, P.C.

Assembly

CD5d1

Entity

1. CD5d1 (polymer, Thiol state: all disulfide bound), 131 monomers, 14766.40 Da Detail

MGSSHHHHHH SSGLVPRGSH MRLSWYDPDF QARLTRSNSK CQGQLEVYLK DGWHMVCSQS WGRSSKQWED PSQASKVCQR LNCGDPLSLG PFLKTYTPQS SIICYGQLGS FSNCSHSRND MCHSLGLTCL E

Formula weight

14766.4 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS41:SG	1:CYS83:SG
2	disulfide	sing	1:CYS57:SG	1:CYS122:SG
3	disulfide	sing	1:CYS78:SG	1:CYS129:SG
4	disulfide	sing	1:CYS104:SG	1:CYS114: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: 86.3 %, Completeness: 79.6 %, Completeness (bb): 81.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.6 % (1188 of 1493)	79.7 % (622 of 780)	80.4 % (459 of 571)	75.4 % (107 of 142)
Backbone	81.7 % (632 of 774)	82.4 % (220 of 267)	81.4 % (311 of 382)	80.8 % (101 of 125)
Sidechain	78.1 % (655 of 839)	78.4 % (402 of 513)	79.9 % (247 of 309)	35.3 % (6 of 17)
Aromatic	70.7 % (106 of 150)	70.7 % (53 of 75)	69.0 % (49 of 71)	100.0 % (4 of 4)
Methyl	87.5 % (77 of 88)	88.6 % (39 of 44)	86.4 % (38 of 44)

1. CD5d1

MGSSHHHHHH SSGLVPRGSH MRLSWYDPDF QARLTRSNSK CQGQLEVYLK DGWHMVCSQS WGRSSKQWED PSQASKVCQR LNCGDPLSLG PFLKTYTPQS SIICYGQLGS FSNCSHSRND MCHSLGLTCL E

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0

#	Name	Isotope labeling	Concentration
1	CD5d1	[U-15N]	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	200 mM
4	EDTA	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0

#	Name	Isotope labeling	Concentration
7	CD5d1	[U-13C; U-15N]	1 mM
8	EDTA	natural abundance	1 mM
9	sodium phosphate	natural abundance	50 mM
10	sodium chloride	natural abundance	200 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 5.0

#	Name	Isotope labeling	Concentration
13	CD5d1	[U-13C; U-15N]	1 mM
14	EDTA	natural abundance	1 mM
15	sodium phosphate	natural abundance	50 mM
16	sodium chloride	natural abundance	200 mM
17	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.64 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 50 models in PDB: 2JOP, Strand ID: A Detail

Release date

2008-06-26

Citation

Three-dimensional solution structure and conformational plasticity of the N-terminal scavenger receptor cysteine-rich domain of human CD5
Garza-Garcia, A., Esposito, D., Rieping, W., Harris, R., Briggs, C., Brown, M.H., Driscoll, P.C.
J. Mol. Biol. (2008), 378, 129-144, PubMed 18339402 , DOI 10.1016/j.jmb.2008.02.006 , Abstract

Related entities 1. CD5d1, : 1 : 3 : 23 entities Detail

Interaction partners 1. CD5d1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC