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1YYM
Asym. Unit
Info
Asym.Unit (269 KB)
Biol.Unit 1 (135 KB)
Biol.Unit 2 (133 KB)
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(1)
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
Authors
:
C. C. Huang, F. Stricher, L. Martin, J. M. Decker, S. Majeed, P. Barthe, W. A. Hendrickson, J. Robinson, C. Roumestand, J. Sodroski, R. Wyatt, C. Vita, P. D. Kwong
Date
:
25 Feb 05 (Deposition) - 03 May 05 (Release) - 14 Jun 17 (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, F23, Antibody, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. C. Huang, F. Stricher, L. Martin, J. M. Decker, S. Majeed, P. Barthe, W. A. Hendrickson, J. Robinson, C. Roumestand, J. Sodroski, R. Wyatt, G. M. Shaw, C. Vita, P. D. Kwong
Scorpion-Toxin Mimics Of Cd4 In Complex With Human Immunodeficiency Virus Gp120 Crystal Structures, Molecular Mimicry, And Neutralization Breadth.
Structure V. 13 755 2005
[
close entry info
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Hetero Components
(6, 24)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
2a: ISOPROPYL ALCOHOL (IPAa)
2b: ISOPROPYL ALCOHOL (IPAb)
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)
4o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
6a: VALINYLAMINE (VLMa)
6b: VALINYLAMINE (VLMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
2
IPA
2
Ligand/Ion
ISOPROPYL ALCOHOL
3
MPT
2
Mod. Amino Acid
BETA-MERCAPTOPROPIONIC ACID
4
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6
VLM
2
Mod. Amino Acid
VALINYLAMINE
[
close Hetero Component info
]
Sites
(20, 20)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:88 , ASN G:241 , NAG G:741 , HOH G:999 , HOH G:1004 , HOH G:1029
BINDING SITE FOR RESIDUE NAG G 588
02
AC2
SOFTWARE
ASN G:234 , THR G:236
BINDING SITE FOR RESIDUE NDG G 734
03
AC3
SOFTWARE
THR G:240 , ASN G:241 , NAG G:588 , HOH G:914
BINDING SITE FOR RESIDUE NAG G 741
04
AC4
SOFTWARE
ARG G:252 , VAL G:254 , ASN G:262 , ASN G:377 , CYS G:378 , SER G:446 , SER G:447 , HOH G:1006
BINDING SITE FOR RESIDUE NAG G 762
05
AC5
SOFTWARE
ASN G:276 , THR G:278 , ASN G:279 , HOH G:1001
BINDING SITE FOR RESIDUE NAG G 776
06
AC6
SOFTWARE
GLU G:269 , ILE G:270 , ASN G:289 , GLU G:290 , GLN G:344 , LYS G:348 , HOH G:927 , HOH G:946 , LYS L:188
BINDING SITE FOR RESIDUE NAG G 789
07
AC7
SOFTWARE
GLU G:87 , ASN G:295 , SER G:446 , HOH G:983
BINDING SITE FOR RESIDUE NAG G 795
08
AC8
SOFTWARE
ASN G:386 , THR G:388 , GLN G:389 , HOH G:954 , GLY S:1014 , LEU S:1015 , LEU S:1016 , VLM S:1027
BINDING SITE FOR RESIDUE NAG G 886
09
AC9
SOFTWARE
HOH P:253 , ASN P:1088 , THR P:1240 , ASN P:1241 , NAG P:1741
BINDING SITE FOR RESIDUE NAG P 1588
10
BC1
SOFTWARE
ASN P:1234 , THR P:1236
BINDING SITE FOR RESIDUE NAG P 1734
11
BC2
SOFTWARE
HOH P:208 , ASP P:1230 , LYS P:1231 , ASN P:1241 , NAG P:1588 , LYS Q:1188
BINDING SITE FOR RESIDUE NAG P 1741
12
BC3
SOFTWARE
HOH P:550 , HOH P:571 , HOH P:785 , VAL P:1254 , ASN P:1262 , ASN P:1377 , CYS P:1378 , SER P:1446 , SER P:1447
BINDING SITE FOR RESIDUE NAG P 1762
13
BC4
SOFTWARE
LYS G:460 , HOH P:236 , ASN P:1276 , THR P:1278 , ASN P:1279
BINDING SITE FOR RESIDUE NAG P 1776
14
BC5
SOFTWARE
HOH P:243 , GLU P:1268 , GLU P:1269 , ILE P:1270 , ASN P:1289 , GLN P:1344 , GLY Q:1212
BINDING SITE FOR RESIDUE NAG P 1789
15
BC6
SOFTWARE
HOH P:656 , GLU P:1087 , ASN P:1295 , SER P:1446
BINDING SITE FOR RESIDUE NAG P 1795
16
BC7
SOFTWARE
HOH P:274 , ASN P:1386 , THR P:1388 , GLN P:1389
BINDING SITE FOR RESIDUE NAG P 1886
17
BC8
SOFTWARE
PRO G:253 , VAL G:254 , LEU G:261 , ASN G:478 , TRP G:479 , HOH G:911
BINDING SITE FOR RESIDUE EDO G 903
18
BC9
SOFTWARE
SER M:12
BINDING SITE FOR RESIDUE EDO M 904
19
CC1
SOFTWARE
SER G:375 , PHE G:376 , TYR G:384 , PHE M:23
BINDING SITE FOR RESIDUE IPA G 901
20
CC2
SOFTWARE
HOH P:64 , VAL P:1255 , SER P:1375 , PHE P:1376 , ASN P:1377
BINDING SITE FOR RESIDUE IPA P 902
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
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_d1yymh2 (H:114-214)
1b: SCOP_d1yymr2 (R:1114-1214)
2a: SCOP_d1yyml2 (L:108-212)
2b: SCOP_d1yymq2 (Q:1108-1212)
3a: SCOP_d1yymh1 (H:1-113)
3b: SCOP_d1yymr1 (R:1001-1113)
4a: SCOP_d1yyml1 (L:1-107)
4b: SCOP_d1yymq1 (Q:1001-1107)
5a: SCOP_d1yymg_ (G:)
5b: SCOP_d1yymp_ (P:)
6a: SCOP_d1yymm1 (M:2-27)
6b: SCOP_d1yyms1 (S:1002-1027)
View:
Select:
Label:
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
d1yymh2
H:114-214
1b
d1yymr2
R:1114-1214
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1yyml2
L:108-212
2b
d1yymq2
Q:1108-1212
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
d1yymh1
H:1-113
3b
d1yymr1
R:1001-1113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
4a
d1yyml1
L:1-107
4b
d1yymq1
Q:1001-1107
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
gp120 core
(24)
Superfamily
:
gp120 core
(24)
Family
:
gp120 core
(24)
Protein domain
:
automated matches
(5)
Human immunodeficiency virus 1 [TaxId: 11676]
(4)
5a
d1yymg_
G:
5b
d1yymp_
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
d1yymm1
M:2-27
6b
d1yyms1
S:1002-1027
[
close SCOP info
]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_1yymG00 (G:83-492)
1b: CATH_1yymP00 (P:1083-1492)
2a: CATH_1yymL02 (L:109-211)
2b: CATH_1yymQ02 (Q:1109-1211)
2c: CATH_1yymH02 (H:114-213)
2d: CATH_1yymR02 (R:1114-1213)
2e: CATH_1yymH01 (H:1-113)
2f: CATH_1yymR01 (R:1001-1113)
2g: CATH_1yymL01 (L:1-108)
2h: CATH_1yymQ01 (Q:1001-1108)
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 1. Organism_taxid: 11676.
(3)
1a
1yymG00
G:83-492
1b
1yymP00
P:1083-1492
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human immunodeficiency virus 1. Organism_taxid: 11676.
(3)
2a
1yymL02
L:109-211
2b
1yymQ02
Q:1109-1211
2c
1yymH02
H:114-213
2d
1yymR02
R:1114-1213
2e
1yymH01
H:1-113
2f
1yymR01
R:1001-1113
2g
1yymL01
L:1-108
2h
1yymQ01
Q:1001-1108
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_GP120_1yymP01 (P:1083-1492)
1b: PFAM_GP120_1yymP02 (P:1083-1492)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: GP120]
(26)
Family
:
GP120
(26)
Human immunodeficiency virus type 1 group M subtype B (isolate YU-2) (HIV-1)
(3)
1a
GP120-1yymP01
P:1083-1492
1b
GP120-1yymP02
P:1083-1492
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Asymmetric Unit 1
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Asym.Unit (269 KB)
Header - Asym.Unit
Biol.Unit 1 (135 KB)
Header - Biol.Unit 1
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