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2I5Y
Asym. Unit
Info
Asym.Unit (264 KB)
Biol.Unit 1 (133 KB)
Biol.Unit 2 (130 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CD4M47, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B
Authors
:
C. -C. Huang, P. D. Kwong
Date
:
26 Aug 06 (Deposition) - 10 Oct 06 (Release) - 06 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : G,H,L,M,P,Q,R,S
Biol. Unit 1: G,H,L,M (1x)
Biol. Unit 2: P,Q,R,S (1x)
Keywords
:
Hiv-1, Gp120, Yu2, Scorpion Toxin, Cd4 Mimic, Cd4M47, Antibody, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Stricher, C. C. Huang, A. Descours, S. Duquesnoy, O. Combes, J. M. Decker, Y. D. Kwon, P. Lusso, G. M. Shaw, C. Vita, P. D. Kwong, L. Martin
Combinatorial Optimization Of A Cd4-Mimetic Miniprotein And Cocrystal Structures With Hiv-1 Gp120 Envelope Glycoprotein
J. Mol. Biol. V. 382 510 2008
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Hetero Components
(6, 24)
Info
All Hetero Components
1a: (R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)... (BIFa)
1b: (R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)... (BIFb)
2a: D-PROLINE (DPRa)
2b: D-PROLINE (DPRb)
3a: BETA-MERCAPTOPROPIONIC ACID (MPTa)
3b: BETA-MERCAPTOPROPIONIC ACID (MPTb)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
6a: VALINYLAMINE (VLMa)
6b: VALINYLAMINE (VLMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BIF
2
Mod. Amino Acid
(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC ACID
2
DPR
2
Mod. Amino Acid
D-PROLINE
3
MPT
2
Mod. Amino Acid
BETA-MERCAPTOPROPIONIC ACID
4
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6
VLM
2
Mod. Amino Acid
VALINYLAMINE
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:88 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 588
02
AC2
SOFTWARE
ASN G:234 , THR G:236 , SER G:274 , HOH G:950
BINDING SITE FOR RESIDUE NAG G 734
03
AC3
SOFTWARE
ASP G:230 , LYS G:231 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 741
04
AC4
SOFTWARE
ARG G:252 , ASN G:262 , ASN G:377 , CYS G:378 , CYS G:445 , SER G:446 , SER G:447 , HOH G:942
BINDING SITE FOR RESIDUE NAG G 762
05
AC5
SOFTWARE
ASN G:276 , THR G:278 , ASN G:279 , LYS P:460
BINDING SITE FOR RESIDUE NAG G 776
06
AC6
SOFTWARE
GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLU G:290 , GLN G:344 , LYS L:188
BINDING SITE FOR RESIDUE NAG G 789
07
AC7
SOFTWARE
GLU G:87 , ASN G:295 , SER G:446
BINDING SITE FOR RESIDUE NAG G 795
08
AC8
SOFTWARE
ASN G:386 , THR G:388 , GLY S:14
BINDING SITE FOR RESIDUE NAG G 886
09
AC9
SOFTWARE
ASN P:88 , THR P:240 , ASN P:241 , NDG P:741 , HOH P:932
BINDING SITE FOR RESIDUE NAG P 588
10
BC1
SOFTWARE
ASN P:234 , THR P:236
BINDING SITE FOR RESIDUE NAG P 734
11
BC2
SOFTWARE
ASP P:230 , LYS P:231 , ASN P:241 , NAG P:588
BINDING SITE FOR RESIDUE NDG P 741
12
BC3
SOFTWARE
ASN P:262 , ASN P:377 , CYS P:378 , SER P:446 , SER P:447 , HOH P:905 , HOH P:920
BINDING SITE FOR RESIDUE NAG P 762
13
BC4
SOFTWARE
LYS G:460 , ASN P:276 , THR P:278 , ASN P:279
BINDING SITE FOR RESIDUE NAG P 776
14
BC5
SOFTWARE
GLU P:267 , GLU P:268 , GLU P:269 , ILE P:270 , ASN P:289 , GLN P:344
BINDING SITE FOR RESIDUE NDG P 789
15
BC6
SOFTWARE
GLU P:87 , ASN P:295 , SER P:446
BINDING SITE FOR RESIDUE NAG P 795
16
BC7
SOFTWARE
ASP G:461 , THR G:462 , ASN P:386 , THR P:388 , GLN P:389
BINDING SITE FOR RESIDUE NAG P 886
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(6, 12)
Info
All SCOP Domains
1a: SCOP_d2i5yh2 (H:114-214)
1b: SCOP_d2i5yr2 (R:114-214)
2a: SCOP_d2i5yl2 (L:108-212)
2b: SCOP_d2i5yq2 (Q:108-212)
3a: SCOP_d2i5yh1 (H:1-113)
3b: SCOP_d2i5yr1 (R:1-113)
4a: SCOP_d2i5yl1 (L:1-107)
4b: SCOP_d2i5yq1 (Q:1-107)
5a: SCOP_d2i5yg_ (G:)
5b: SCOP_d2i5yp_ (P:)
6a: SCOP_d2i5ym1 (M:2-27)
6b: SCOP_d2i5ys1 (S:2-27)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
1a
d2i5yh2
H:114-214
1b
d2i5yr2
R:114-214
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d2i5yl2
L:108-212
2b
d2i5yq2
Q:108-212
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(37)
3a
d2i5yh1
H:1-113
3b
d2i5yr1
R:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
4a
d2i5yl1
L:1-107
4b
d2i5yq1
Q:1-107
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
gp120 core
(24)
Superfamily
:
gp120 core
(24)
Family
:
gp120 core
(24)
Protein domain
:
gp120 core
(19)
Human immunodeficiency virus [TaxId: 12721]
(1)
5a
d2i5yg_
G:
5b
d2i5yp_
P:
Class
:
Designed proteins
(167)
Fold
:
Scorpion toxin-based designs
(6)
Superfamily
:
Scorpion toxin-based designs
(6)
Family
:
Mini-protein reproducing the core of the CD4 surface
(5)
Protein domain
:
Mini-protein reproducing the core of the CD4 surface
(5)
Synthetic
(5)
6a
d2i5ym1
M:2-27
6b
d2i5ys1
S:2-27
[
close SCOP info
]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_2i5yG00 (G:82-492)
1b: CATH_2i5yP00 (P:82-492)
2a: CATH_2i5yL02 (L:109-211)
2b: CATH_2i5yQ02 (Q:109-211)
2c: CATH_2i5yL01 (L:1-108)
2d: CATH_2i5yQ01 (Q:1-108)
2e: CATH_2i5yH02 (H:114-213)
2f: CATH_2i5yR02 (R:114-213)
2g: CATH_2i5yH01 (H:1-113)
2h: CATH_2i5yR01 (R:1-113)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
HIV Envelope Protein Gp120; Chain G
(17)
Homologous Superfamily
:
HIV Envelope Protein Gp120; Chain G
(17)
Human immunodeficiency virus. Organism_taxid: 12721. Strain: yu2.
(1)
1a
2i5yG00
G:82-492
1b
2i5yP00
P:82-492
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human immunodeficiency virus. Organism_taxid: 12721. Strain: yu2.
(1)
2a
2i5yL02
L:109-211
2b
2i5yQ02
Q:109-211
2c
2i5yL01
L:1-108
2d
2i5yQ01
Q:1-108
2e
2i5yH02
H:114-213
2f
2i5yR02
R:114-213
2g
2i5yH01
H:1-113
2h
2i5yR01
R:1-113
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (264 KB)
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