Cyclic Peptide DataBank (CPDB)

Summary

PDB ID	1YYM Go to RCSB ➚
Title	crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b
Method	X-RAY DIFFRACTION
Resolution	2.20 Å
R-factors	R-work: 0.209, R-free: 0.268
Release Date	2005-05-03
Authors	Huang, C.C.; Stricher, F.; Martin, L.; Decker, J.M.; Majeed, S.; Barthe, P.; Hendrickson, W.A.; Robinson, J.; Roumestand, C.; Sodroski, J.; Wyatt, R.; Shaw, G.M.; Vita, C.; Kwong, P.D.
Source Organism	Homo sapiens, Human immunodeficiency virus 1, synthetic construct
Expression Host	Drosophila melanogaster, Mus musculus
Keywords	HIV-1, gp120, YU2, scorpion toxin, CD4 mimic, F23, antibody, Viral protein-Immune system COMPLEX
Molecular Weight	174.90 kDa
Entity Count	Protein: 4, Nucleic Acid: 0, NA Hybrid: 0
Space Group	P 1 21 1
Cell Parameters	a=51.62 Å, b=157.04 Å, c=108.93 Å, α=90.00°, β=93.45°, γ=90.00°
Disulfide Bond	M6-M24;M10-M26;S1006-S1024;S1010-S1026
Other Links	Yes
Peptide Chains	M, S
Protein Chains	G, H, L, P, Q, R
Peptide Lengths	27
Protein Lengths	313, 214, 229

Sequence Information

Chain: G, P - Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120) (Length: 313)

1	GARSEVKLEN VTENFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVG AGSCNTSVIT
61	QACPKVSFEP IPIHYCAPAG FAILKCNDKK FNGTGPCTNV STVQCTHGIR PVVSTQLLLN
121	GSLAEEEIVI RSENFTNNAK TIIVQLNESV VINCTGAGHC NLSKTQWENT LEQIAIKLKE
181	QFGNNKTIIF NPSSGGDPEI VTHSFNCGGE FFYCNSTQLF TWNDTRKLNN TGRNITLPCR
241	IKQIINMWQE VGKAMYAPPI RGQIRCSSNI TGLLLTRDGG KDTNGTEIFR PGGGDMRDNW
301	RSELYKYKVV KIE

Chain: L, Q - antibody 17b light chain (Length: 214)

1	DIVMTQSPAT LSVSPGERAT LSCRASESVS SDLAWYQQKP GQAPRLLIYG ASTRATGVPA
61	RFSGSGSGAE FTLTISSLQS EDFAVYYCQQ YNNWPPRYTF GQGTRLEIKR TVAAPSVFIF
121	PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST
181	LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRG

Chain: H, R - antibody 17b heavy chain (Length: 229)

1	EVQLVESGAE VKKPGSSVKV SCKASGDTFI RYSFTWVRQA PGQGLEWMGR IITILDVAHY
61	APHLQGRVTI TADKSTSTVY LELRNLRSDD TAVYFCAGVY EGEADEGEYD NNGFLKHWGQ
121	GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT
181	FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPK

Chain: M, S - F23, scorpion-toxin mimic of CD4 (Length: 27)

1	XNLHFCQLRC KSLGLLGKCA GSFCACX

References

Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth.

Huang, C.C., Stricher, F., Martin, L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson, W.A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G.M., Vita, C., Kwong, P.D.

Structure, 2005

PubMed: 15893666 | DOI: 10.1016/j.str.2005.03.006

Ligand Information

ID	Name	Formula	Molecular Weight
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	221.208
IPA	ISOPROPYL ALCOHOL	C3 H8 O	60.095
EDO	1,2-ETHANEDIOL	C2 H6 O2	62.068

Biological Assemblies

Assembly ID: 1

Details: author_defined_assembly

Oligomeric State: Hetero 4-mer

Stoichiometry: A1, B1, C1, D1

Assembly ID: 2