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1HZH
Asym. Unit
Info
Asym.Unit (219 KB)
Biol.Unit 1 (211 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE INTACT HUMAN IGG B12 WITH BROAD AND POTENT ACTIVITY AGAINST PRIMARY HIV-1 ISOLATES: A TEMPLATE FOR HIV VACCINE DESIGN
Authors
:
E. O. Saphire, D. R. Burton, I. A. Wilson
Date
:
24 Jan 01 (Deposition) - 15 Aug 01 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : H,K,L,M
Biol. Unit 1: H,K,L,M (1x)
Keywords
:
Immunoglobulin, Antibody, B12, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. O. Saphire, P. W. Parren, R. Pantophlet, M. B. Zwick, G. M. Morris, P. M. Rudd, R. A. Dwek, R. L. Stanfield, D. R. Burton, I. A. Wilson
Crystal Structure Of A Neutralizing Human Igg Against Hiv-1 A Template For Vaccine Design.
Science V. 293 1155 2001
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Hetero Components
(5, 18)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: ALPHA-L-FUCOSE (FUCa)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
GAL
3
Ligand/Ion
BETA-D-GALACTOSE
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP H:278 , GLN H:312 , ASN H:314 , THR H:318 , NAG H:480
BINDING SITE FOR RESIDUE NAG H 479
02
AC2
SOFTWARE
PHE H:254 , VAL H:277 , NAG H:479 , BMA H:481
BINDING SITE FOR RESIDUE NAG H 480
03
AC3
SOFTWARE
PHE H:254 , NAG H:480 , MAN H:482 , MAN H:485 , MAN K:482
BINDING SITE FOR RESIDUE BMA H 481
04
AC4
SOFTWARE
BMA H:481 , NAG H:483
BINDING SITE FOR RESIDUE MAN H 482
05
AC5
SOFTWARE
MAN H:482 , GAL H:484
BINDING SITE FOR RESIDUE NAG H 483
06
AC6
SOFTWARE
NAG H:483
BINDING SITE FOR RESIDUE GAL H 484
07
AC7
SOFTWARE
BMA H:481 , NAG H:486
BINDING SITE FOR RESIDUE MAN H 485
08
AC8
SOFTWARE
PHE H:256 , LYS H:259 , ARG H:320 , MAN H:485 , GAL H:487
BINDING SITE FOR RESIDUE NAG H 486
09
AC9
SOFTWARE
PHE H:256 , LYS H:259 , GLU H:271 , THR H:273 , NAG H:486
BINDING SITE FOR RESIDUE GAL H 487
10
BC1
SOFTWARE
VAL K:277 , ASP K:278 , GLN K:312 , ASN K:314 , NAG K:480 , FUC K:487
BINDING SITE FOR RESIDUE NAG K 479
11
BC2
SOFTWARE
VAL K:277 , ARG K:320 , NAG K:479 , BMA K:481 , MAN K:484 , FUC K:487
BINDING SITE FOR RESIDUE NAG K 480
12
BC3
SOFTWARE
PHE K:254 , PHE K:256 , NAG K:480 , MAN K:482 , MAN K:484
BINDING SITE FOR RESIDUE BMA K 481
13
BC4
SOFTWARE
BMA H:481 , BMA K:481 , NAG K:483 , HOH K:497
BINDING SITE FOR RESIDUE MAN K 482
14
BC5
SOFTWARE
MAN K:482
BINDING SITE FOR RESIDUE NAG K 483
15
BC6
SOFTWARE
PHE K:256 , NAG K:480 , BMA K:481 , NAG K:485 , FUC K:487
BINDING SITE FOR RESIDUE MAN K 484
16
BC7
SOFTWARE
THR K:273 , MAN K:484 , GAL K:486
BINDING SITE FOR RESIDUE NAG K 485
17
BC8
SOFTWARE
GLU K:271 , THR K:273 , NAG K:485
BINDING SITE FOR RESIDUE GAL K 486
18
BC9
SOFTWARE
NAG K:479 , NAG K:480 , MAN K:484
BINDING SITE FOR RESIDUE FUC K 487
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066403 (W148R, chain L/M, )
2: VAR_003897 (V191L, chain L/M, )
3: VAR_003886 (K222R, chain H/K, )
4: VAR_003887 (D377E, chain H/K, )
5: VAR_003888 (L381M, chain H/K, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
L/M
W
148
R
2
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
L/M
V
191
L
3
UniProt
VAR_003886
K
97
R
IGHG1_HUMAN
Unclassified
---
H/K
K
222
R
4
UniProt
VAR_003887
D
239
E
IGHG1_HUMAN
Unclassified
---
H/K
D
377
E
5
UniProt
VAR_003888
L
241
M
IGHG1_HUMAN
Unclassified
---
H/K
L
381
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (H:206-212,K:206-212|H:454-460,K:45...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGHG1_HUMAN
81-87
306-312
4
H:206-212
K:206-212
H:454-460
K:454-460
IGKC_HUMAN
85-91
2
L:192-198
M:192-198
IGG1_HUMAN
200-206
425-431
4
H:206-212
K:206-212
H:454-460
K:454-460
[
close PROSITE info
]
Exons
(4, 8)
Info
All Exons
Exon 1.1 (H:114-226 (gaps) | K:114-226 (gaps...)
Exon 1.2 (H:226-244 (gaps) | K:226-244 (gaps...)
Exon 1.3b (H:244-361 (gaps) | K:244-361 (gaps...)
Exon 1.4c (H:361-478 (gaps) | K:361-475 (gaps...)
View:
Select:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3b
4: Boundary 1.3b/1.4c
5: Boundary 1.4c/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000390549
1
ENSE00001838294
chr14:
106209408-106209114
295
IGHG1_HUMAN
1-99
99
2
H:114-226 (gaps)
K:114-226 (gaps)
113
113
1.2
ENST00000390549
2
ENSE00001719055
chr14:
106208722-106208678
45
IGHG1_HUMAN
99-114
16
2
H:226-244 (gaps)
K:226-244 (gaps)
19
19
1.3b
ENST00000390549
3b
ENSE00001776617
chr14:
106208559-106208230
330
IGHG1_HUMAN
114-224
111
2
H:244-361 (gaps)
K:244-361 (gaps)
118
118
1.4c
ENST00000390549
4c
ENSE00001837466
chr14:
106208132-106207675
458
IGHG1_HUMAN
224-330
107
2
H:361-478 (gaps)
K:361-475 (gaps)
118
115
[
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]
SCOP Domains
(6, 12)
Info
All SCOP Domains
1a: SCOP_d1hzhh2 (H:114-235)
1b: SCOP_d1hzhk2 (K:114-235)
2a: SCOP_d1hzhh3 (H:236-359)
2b: SCOP_d1hzhk3 (K:239-359)
3a: SCOP_d1hzhh4 (H:360-478)
3b: SCOP_d1hzhk4 (K:360-475)
4a: SCOP_d1hzhl2 (L:108-214)
4b: SCOP_d1hzhm2 (M:108-214)
5a: SCOP_d1hzhh1 (H:1-113)
5b: SCOP_d1hzhk1 (K:1-113)
6a: SCOP_d1hzhl1 (L:1-107)
6b: SCOP_d1hzhm1 (M:1-107)
View:
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Classes
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)
(
)
Folds
(
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(
)
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
d1hzhh2
H:114-235
1b
d1hzhk2
K:114-235
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 2, CH2-gamma
(36)
Human (Homo sapiens) [TaxId: 9606]
(31)
2a
d1hzhh3
H:236-359
2b
d1hzhk3
K:239-359
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma
(38)
Human (Homo sapiens) [TaxId: 9606]
(31)
3a
d1hzhh4
H:360-478
3b
d1hzhk4
K:360-475
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
4a
d1hzhl2
L:108-214
4b
d1hzhm2
M:108-214
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)
5a
d1hzhh1
H:1-113
5b
d1hzhk1
K:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 3.1 [TaxId: 9606]
(8)
6a
d1hzhl1
L:1-107
6b
d1hzhm1
M:1-107
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1hzhL02 (L:108-211)
1b: CATH_1hzhL01 (L:1-107)
1c: CATH_1hzhM01 (M:1-108)
1d: CATH_1hzhK02 (K:105-230)
1e: CATH_1hzhH04 (H:361-474)
1f: CATH_1hzhK04 (K:361-473)
1g: CATH_1hzhK01 (K:1-104)
1h: CATH_1hzhH03 (H:250-360)
1i: CATH_1hzhK03 (K:250-360)
1j: CATH_1hzhH02 (H:129-236)
1k: CATH_1hzhH01 (H:24-128)
1l: CATH_1hzhM02 (M:109-211)
View:
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Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
1hzhL02
L:108-211
1b
1hzhL01
L:1-107
1c
1hzhM01
M:1-108
1d
1hzhK02
K:105-230
1e
1hzhH04
H:361-474
1f
1hzhK04
K:361-473
1g
1hzhK01
K:1-104
1h
1hzhH03
H:250-360
1i
1hzhK03
K:250-360
1j
1hzhH02
H:129-236
1k
1hzhH01
H:24-128
1l
1hzhM02
M:109-211
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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Asym.Unit (219 KB)
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