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1YYL
Asym. Unit
Info
Asym.Unit (260 KB)
Biol.Unit 1 (130 KB)
Biol.Unit 2 (129 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CD4M33, 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
:
2.75
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, Cd4M33, 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
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Hetero Components
(5, 22)
Info
All Hetero Components
1a: (R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)... (BIFa)
1b: (R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)... (BIFb)
2a: BETA-MERCAPTOPROPIONIC ACID (MPTa)
2b: BETA-MERCAPTOPROPIONIC ACID (MPTb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5a: VALINYLAMINE (VLMa)
5b: 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
MPT
2
Mod. Amino Acid
BETA-MERCAPTOPROPIONIC ACID
3
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5
VLM
2
Mod. Amino Acid
VALINYLAMINE
[
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]
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 , NAG G:741
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
ASN G:241 , NAG G:588
BINDING SITE FOR RESIDUE NAG G 741
04
AC4
SOFTWARE
ARG G:252 , ASN G:262 , ASN G:377 , CYS G:378 , SER G:446 , SER G:447
BINDING SITE FOR RESIDUE NAG G 762
05
AC5
SOFTWARE
ASN G:276 , THR G:278 , ASN G:279
BINDING SITE FOR RESIDUE NAG G 776
06
AC6
SOFTWARE
GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344 , LYS L:188
BINDING SITE FOR RESIDUE NAG G 789
07
AC7
SOFTWARE
GLU G:87 , ASN G:295
BINDING SITE FOR RESIDUE NAG G 795
08
AC8
SOFTWARE
ASN G:386 , THR G:388 , GLN G:389 , GLY S:1014 , LEU S:1015
BINDING SITE FOR RESIDUE NAG G 886
09
AC9
SOFTWARE
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
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
ARG P:1252 , ASN P:1262 , SER P:1446 , SER P:1447
BINDING SITE FOR RESIDUE NAG P 1762
13
BC4
SOFTWARE
LYS G:460 , ASN P:1276 , THR P:1278 , ASN P:1279
BINDING SITE FOR RESIDUE NAG P 1776
14
BC5
SOFTWARE
GLU P:1267 , GLU P:1268 , GLU P:1269 , ILE P:1270 , ASN P:1289 , GLY Q:1212
BINDING SITE FOR RESIDUE NAG P 1789
15
BC6
SOFTWARE
GLU P:1087 , ASN P:1295 , SER P:1446
BINDING SITE FOR RESIDUE NAG P 1795
16
BC7
SOFTWARE
ASP G:461 , ASN P:1386 , THR P:1388
BINDING SITE FOR RESIDUE NAG P 1886
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
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
View:
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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_d1yylh2 (H:114-214)
1b: SCOP_d1yylr2 (R:1114-1214)
2a: SCOP_d1yyll2 (L:108-212)
2b: SCOP_d1yylq2 (Q:1108-1212)
3a: SCOP_d1yylh1 (H:1-113)
3b: SCOP_d1yylr1 (R:1001-1113)
4a: SCOP_d1yyll1 (L:1-107)
4b: SCOP_d1yylq1 (Q:1001-1107)
5a: SCOP_d1yylg_ (G:)
5b: SCOP_d1yylp_ (P:)
6a: SCOP_d1yylm1 (M:2-27)
6b: SCOP_d1yyls1 (S:1002-1027)
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(
)
(
)
Folds
(
)
(
)
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(
)
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
d1yylh2
H:114-214
1b
d1yylr2
R:1114-1214
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1yyll2
L:108-212
2b
d1yylq2
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
d1yylh1
H:1-113
3b
d1yylr1
R:1001-1113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.2 [TaxId: 9606]
(31)
4a
d1yyll1
L:1-107
4b
d1yylq1
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
d1yylg_
G:
5b
d1yylp_
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
d1yylm1
M:2-27
6b
d1yyls1
S:1002-1027
[
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]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_1yylG00 (G:83-492)
1b: CATH_1yylP00 (P:1083-1492)
2a: CATH_1yylL02 (L:109-211)
2b: CATH_1yylH02 (H:114-213)
2c: CATH_1yylR02 (R:1114-1213)
2d: CATH_1yylH01 (H:1-113)
2e: CATH_1yylR01 (R:1001-1113)
2f: CATH_1yylQ02 (Q:1109-1211)
2g: CATH_1yylL01 (L:1-108)
2h: CATH_1yylQ01 (Q:1001-1108)
View:
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Classes
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)
(
)
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
1yylG00
G:83-492
1b
1yylP00
P:1083-1492
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human immunodeficiency virus 1. Organism_taxid: 11676.
(3)
2a
1yylL02
L:109-211
2b
1yylH02
H:114-213
2c
1yylR02
R:1114-1213
2d
1yylH01
H:1-113
2e
1yylR01
R:1001-1113
2f
1yylQ02
Q:1109-1211
2g
1yylL01
L:1-108
2h
1yylQ01
Q:1001-1108
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_GP120_1yylP01 (P:1083-1492)
1b: PFAM_GP120_1yylP02 (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
GP120-1yylP01
P:1083-1492
1b
GP120-1yylP02
P:1083-1492
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Asym.Unit (260 KB)
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