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2QAD
Biol. Unit 3
Info
Asym.Unit (667 KB)
Biol.Unit 1 (334 KB)
Biol.Unit 2 (330 KB)
Biol.Unit 3 (657 KB)
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(1)
Title
:
STRUCTURE OF TYROSINE-SULFATED 412D ANTIBODY COMPLEXED WITH HIV-1 YU2 GP120 AND CD4
Authors
:
C. -C. Huang, M. Tang, J. Robinson, R. Wyatt, P. D. Kwong
Date
:
14 Jun 07 (Deposition) - 25 Sep 07 (Release) - 29 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: A,B,C,D,E,F,G,H (1x)
Keywords
:
Viral Protein/Immune System, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. -C. Huang, S. N. Lam, P. Acharya, M. Tang, S. -H. Xiang, S. S. Hussan, R. L. Stanfield, J. Robinson, J. Sodroski, I. A. Wilson, R. Wyatt, C. A. Bewley, P. D. Kwong
Structures Of The Ccr5 N Terminus And Of A Tyrosine-Sulfate Antibody With Hiv-1 Gp120 And Cd4
Science V. 317 1930 2007
[
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Hetero Components
(4, 46)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
2a: MALONIC ACID (MLAa)
2b: MALONIC ACID (MLAb)
2c: MALONIC ACID (MLAc)
2d: MALONIC ACID (MLAd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
3ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
3ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
3ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
3ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
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)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
3z: N-ACETYL-D-GLUCOSAMINE (NAGz)
4a: O-SULFO-L-TYROSINE (TYSa)
4b: O-SULFO-L-TYROSINE (TYSb)
4c: O-SULFO-L-TYROSINE (TYSc)
4d: O-SULFO-L-TYROSINE (TYSd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
2
MLA
4
Ligand/Ion
MALONIC ACID
3
NAG
31
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
TYS
4
Mod. Amino Acid
O-SULFO-L-TYROSINE
[
close Hetero Component info
]
Sites
(37, 37)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:234 , THR A:236
BINDING SITE FOR RESIDUE NAG A 734
02
AC2
SOFTWARE
ASN A:241
BINDING SITE FOR RESIDUE NAG A 741
03
AC3
SOFTWARE
PRO A:212 , ARG A:252 , LEU A:261 , ASN A:262 , ASN A:377 , CYS A:445 , SER A:447
BINDING SITE FOR RESIDUE NAG A 762
04
AC4
SOFTWARE
ASN A:276 , ASN A:279
BINDING SITE FOR RESIDUE NAG A 776
05
AC5
SOFTWARE
GLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , LYS C:126
BINDING SITE FOR RESIDUE NAG A 789
06
AC6
SOFTWARE
ASN A:295 , ARG A:444 , SER A:446 , NAG E:795 , NAG E:832 , NAG E:913
BINDING SITE FOR RESIDUE NAG A 795
07
AC7
SOFTWARE
ASN A:301
BINDING SITE FOR RESIDUE NAG A 801
08
AC8
SOFTWARE
THR A:297 , HIS A:330 , ASN A:332 , ASN A:413 , NAG A:913
BINDING SITE FOR RESIDUE NAG A 832
09
AC9
SOFTWARE
ASN A:356
BINDING SITE FOR RESIDUE NAG A 856
10
BC1
SOFTWARE
ASN A:362 , PRO A:363 , SER A:364 , SER A:365 , ARG A:469
BINDING SITE FOR RESIDUE NAG A 862
11
BC2
SOFTWARE
ASN A:386 , THR A:388 , GLN A:389
BINDING SITE FOR RESIDUE NAG A 886
12
BC3
SOFTWARE
ILE A:360 , PHE A:361 , ASN A:362 , ASN A:394 , ARG A:397
BINDING SITE FOR RESIDUE NAG A 894
13
BC4
SOFTWARE
ASN A:400 , ASP C:151 , ASN C:152 , LEU C:191
BINDING SITE FOR RESIDUE NAG A 900
14
BC5
SOFTWARE
SER A:334 , ARG A:412 , ASN A:413 , NAG A:832 , NAG E:795
BINDING SITE FOR RESIDUE NAG A 913
15
BC6
SOFTWARE
SER A:291 , ASN A:448
BINDING SITE FOR RESIDUE NAG A 948
16
BC7
SOFTWARE
ASN A:463
BINDING SITE FOR RESIDUE NAG A 963
17
BC8
SOFTWARE
ASN E:234
BINDING SITE FOR RESIDUE NAG E 734
18
BC9
SOFTWARE
ASP E:230 , ASN E:241
BINDING SITE FOR RESIDUE NAG E 741
19
CC1
SOFTWARE
PRO E:212 , VAL E:254 , ASN E:262 , ASN E:377 , CYS E:445 , SER E:446 , SER E:447
BINDING SITE FOR RESIDUE NAG E 762
20
CC2
SOFTWARE
GLU E:275 , ASN E:276
BINDING SITE FOR RESIDUE NAG E 776
21
CC3
SOFTWARE
VAL C:205 , GLU E:268 , GLU E:269 , ASN E:289 , GLU E:290 , GLN E:344
BINDING SITE FOR RESIDUE NAG E 789
22
CC4
SOFTWARE
NAG A:795 , NAG A:913 , ASN E:295 , ARG E:444
BINDING SITE FOR RESIDUE NAG E 795
23
CC5
SOFTWARE
ASN E:301
BINDING SITE FOR RESIDUE NAG E 801
24
CC6
SOFTWARE
NAG A:795 , ASN E:295 , ASN E:332 , THR E:415
BINDING SITE FOR RESIDUE NAG E 832
25
CC7
SOFTWARE
ASN E:356 , GLN H:192 , TYR H:194
BINDING SITE FOR RESIDUE NAG E 856
26
CC8
SOFTWARE
ASN E:362 , PRO E:363 , SER E:364 , NAG E:894
BINDING SITE FOR RESIDUE NAG E 862
27
CC9
SOFTWARE
THR E:240 , VAL E:242 , ASN E:386 , THR E:388
BINDING SITE FOR RESIDUE NAG E 886
28
DC1
SOFTWARE
ASN E:394 , NAG E:862
BINDING SITE FOR RESIDUE NAG E 894
29
DC2
SOFTWARE
NAG A:795 , ASN E:413
BINDING SITE FOR RESIDUE NAG E 913
30
DC3
SOFTWARE
ASN E:262 , SER E:291 , ASN E:448
BINDING SITE FOR RESIDUE NAG E 948
31
DC4
SOFTWARE
ASN E:463 , HIS G:198 , SER G:202
BINDING SITE FOR RESIDUE NAG E 963
32
DC5
SOFTWARE
ARG H:38 , ARG H:62 , GLU H:85 , ASP H:86
BINDING SITE FOR RESIDUE MLA H 215
33
DC6
SOFTWARE
LYS B:2 , VAL B:3 , LYS B:166
BINDING SITE FOR RESIDUE MLA B 186
34
DC7
SOFTWARE
SER F:104
BINDING SITE FOR RESIDUE MLA F 186
35
DC8
SOFTWARE
LYS E:421 , ILE E:491 , GLU E:492
BINDING SITE FOR RESIDUE EDO E 7
36
DC9
SOFTWARE
LYS A:350 , ASN A:355 , ASN A:356 , LYS A:357 , THR A:358
BINDING SITE FOR RESIDUE EDO A 8
37
EC1
SOFTWARE
GLN C:27 , SER C:28
BINDING SITE FOR RESIDUE EDO C 216
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_023459 (K166E, chain B/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_023459
K
191
E
CD4_HUMAN
Polymorphism
28917504
B/F
K
166
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d2qadd2 (D:114-214)
1b: SCOP_d2qadh2 (H:114-214)
2a: SCOP_d2qadb2 (B:98-178)
2b: SCOP_d2qadf2 (F:98-178)
3a: SCOP_d2qadb1 (B:1-97)
3b: SCOP_d2qadf1 (F:1-97)
4a: SCOP_d2qadd1 (D:1-113)
4b: SCOP_d2qadh1 (H:1-113)
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)
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(
)
(
)
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(
)
(
)
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
d2qadd2
D:114-214
1b
d2qadh2
H:114-214
Family
:
C2 set domains
(47)
Protein domain
:
CD4 C2-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
2a
d2qadb2
B:98-178
2b
d2qadf2
F:98-178
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
CD4 V-set domains
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
3a
d2qadb1
B:1-97
3b
d2qadf1
F:1-97
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(37)
4a
d2qadd1
D:1-113
4b
d2qadh1
H:1-113
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2qadC02 (C:110-211)
1b: CATH_2qadD02 (D:110-214)
1c: CATH_2qadH02 (H:110-214)
1d: CATH_2qadD01 (D:1-109)
1e: CATH_2qadH01 (H:1-109)
1f: CATH_2qadB01 (B:1-98)
1g: CATH_2qadF01 (F:1-98)
1h: CATH_2qadB02 (B:99-173)
1i: CATH_2qadF02 (F:99-173)
1j: CATH_2qadG02 (G:110-211)
1k: CATH_2qadC01 (C:1-108)
1l: CATH_2qadG01 (G:1-108)
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(
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(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: yu2.
(2)
1a
2qadC02
C:110-211
1b
2qadD02
D:110-214
1c
2qadH02
H:110-214
1d
2qadD01
D:1-109
1e
2qadH01
H:1-109
1f
2qadB01
B:1-98
1g
2qadF01
F:1-98
1h
2qadB02
B:99-173
1i
2qadF02
F:99-173
1j
2qadG02
G:110-211
1k
2qadC01
C:1-108
1l
2qadG01
G:1-108
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_C2_set_2qadF01 (F:100-178)
1b: PFAM_C2_set_2qadF02 (F:100-178)
2a: PFAM_V_set_2qadF03 (F:1-105)
2b: PFAM_V_set_2qadF04 (F:1-105)
3a: PFAM_GP120_2qadE01 (E:90-492)
3b: PFAM_GP120_2qadE02 (E:90-492)
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Clans
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(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C2-set
(18)
Homo sapiens (Human)
(18)
1a
C2-set-2qadF01
F:100-178
1b
C2-set-2qadF02
F:100-178
Family
:
V-set
(144)
Homo sapiens (Human)
(61)
2a
V-set-2qadF03
F:1-105
2b
V-set-2qadF04
F:1-105
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)
3a
GP120-2qadE01
E:90-492
3b
GP120-2qadE02
E:90-492
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Asym.Unit (667 KB)
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