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BMRB: 25694

2N55

Structure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus

Authors

Ziarek, J.J., Peterson, F.C., Volkman, B.F.

Assembly

CXCL12-CXCR4

Entity

1. CXCL12-CXCR4, entity 1 (polymer, Thiol state: all disulfide bound), 70 monomers, 8131.554 Da Detail

GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCALQI VARLKNNNRQ VCIDPKCKWC QEYLEKALNK

2. CXCL12-CXCR4, entity 2 (polymer, Thiol state: not present), 40 monomers, 4515.745 Da Detail

GSMEGISIYT SDNYTEEMGS GDYDSMKEPA FREENANFNK

Total weight

12647.299 Da

Max. entity weight

8131.554 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.8 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.8 % (1222 of 1303)	95.3 % (656 of 688)	91.7 % (454 of 495)	93.3 % (112 of 120)
Backbone	96.0 % (624 of 650)	96.8 % (213 of 220)	95.7 % (311 of 325)	95.2 % (100 of 105)
Sidechain	92.5 % (701 of 758)	94.7 % (443 of 468)	89.5 % (246 of 275)	80.0 % (12 of 15)
Aromatic	78.0 % (78 of 100)	94.0 % (47 of 50)	61.2 % (30 of 49)	100.0 % (1 of 1)
Methyl	92.0 % (81 of 88)	95.5 % (42 of 44)	88.6 % (39 of 44)

1. entity 1

GMKPVSLSYR CPCRFFESHV ARANVKHLKI LNTPNCALQI VARLKNNNRQ VCIDPKCKWC QEYLEKALNK

2. entity 2

GSMEGISIYT SDNYTEEMGS GDYDSMKEPA FREENANFNK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	2 mM
2	MES	[U-2H]	25 mM
3	D2O	[U-99% 2H]	10 %
4	sodium azide	natural abundance	0.02 %
5	entity_2	natural abundance	2 mM
6	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Concentration
7	entity_2	[U-99% 13C; U-99% 15N]	1 mM
8	MES	[U-2H]	25 mM
9	sodium azide	natural abundance	0.02 %
10	D2O	[U-99% 2H]	10 %
11	entity_1	natural abundance	2 mM
12	H2O	[U-99% 2H]	90 %

LACS Plot; CA

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

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.41 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N55, Strand ID: A, B Detail

Release date

2016-04-24

Citation

Structure-Based Identification of Novel Ligands Targeting Multiple Sites within a Chemokine-G-Protein-Coupled-Receptor Interface
Smith, E.W., Nevins, A.M., Qiao, Z., Liu, Y., Getschman, A.E., Vankayala, S.L., Kemp, M., Peterson, F.C., Li, R., Volkman, B.F., Chen, Y.
J. Med. Chem. (2016), 59, 4342-4351, PubMed 27058821 , DOI 10.1021/acs.jmedchem.5b02042 , Abstract

Related entities 1. CXCL12-CXCR4, entity 1, : 1 : 27 entities Detail

Related entities 2. CXCL12-CXCR4, entity 2, : 1 : 1 : 3 : 21 entities Detail

Experiments performed 8 experiments Detail

1 3D 1H-15N NOESY