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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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3SE9
Asym. Unit
Info
Asym.Unit (397 KB)
Biol.Unit 1 (388 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC-PG04 IN COMPLEX WITH HIV-1 GP120
Authors
:
P. D. Kwong, T. Zhou
Date
:
10 Jun 11 (Deposition) - 10 Aug 11 (Release) - 05 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : G,H,L
Biol. Unit 1: G,H,L (1x)
Keywords
:
Hiv, Gp120, Antibody, Vrc-Pg04, Neutralization, Vaccine, Envelope Glycoprotein, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Wu, T. Zhou, J. Zhu, B. Zhang, I. Georgiev, C. Wang, X. Chen, N. S. Longo, M. Louder, K. Mckee, S. O'Dell, S. Perfetto, S. D. Schmidt, W. Shi, L. Wu, Y. Yang, Z. Y. Yang, Z. Yang, Z. Zhang, M. Bonsignori, J. A. Crump, S. H. Kapiga, N. E. Sam, B. F. Haynes, M. Simek, D. R. Burton, W. C. Koff, N. A. Doria-Rose, M. Connors, J. C. Mullikin, G. J. Nabel, M. Roederer, L. Shapiro, P. D. Kwong, J. R. Mascola
Focused Evolution Of Hiv-1 Neutralizing Antibodies Revealed By Structures And Deep Sequencing.
Science V. 333 1593 2011
[
close entry info
]
Hetero Components
(6, 39)
Info
All Hetero Components
1a: (R,R)-2,3-BUTANEDIOL (BU3a)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
2i: CHLORIDE ION (CLi)
2j: CHLORIDE ION (CLj)
2k: CHLORIDE ION (CLk)
2l: CHLORIDE ION (CLl)
2m: CHLORIDE ION (CLm)
2n: CHLORIDE ION (CLn)
2o: CHLORIDE ION (CLo)
2p: CHLORIDE ION (CLp)
2q: CHLORIDE ION (CLq)
2r: CHLORIDE ION (CLr)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
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)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
6a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BU3
1
Ligand/Ion
(R,R)-2,3-BUTANEDIOL
2
CL
18
Ligand/Ion
CHLORIDE ION
3
GOL
4
Ligand/Ion
GLYCEROL
4
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SO4
5
Ligand/Ion
SULFATE ION
6
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(38, 38)
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)
38: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:234 , THR G:236 , HIS G:352 , HOH G:507 , CL G:1015
BINDING SITE FOR RESIDUE NAG G 734
02
AC2
SOFTWARE
ASN G:229 , LYS G:231 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 741
03
AC3
SOFTWARE
HOH G:6 , LYS G:252 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , HOH G:508 , HOH G:596 , HOH G:650
BINDING SITE FOR RESIDUE NAG G 762
04
AC4
SOFTWARE
ASN G:276 , HOH G:503 , GOL G:1007 , GLY H:100A , GLY H:100C , GLY L:31 , HIS L:32 , LEU L:91
BINDING SITE FOR RESIDUE NAG G 776
05
AC5
SOFTWARE
GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , LYS G:348 , HOH G:577 , HOH G:637 , SO4 G:1002
BINDING SITE FOR RESIDUE NAG G 789
06
AC6
SOFTWARE
ASN G:295 , GLU G:332 , LYS G:442 , HOH G:589 , HOH G:680
BINDING SITE FOR RESIDUE NAG G 795
07
AC7
SOFTWARE
PRO G:79 , PRO G:81 , ASN G:334 , LYS G:337
BINDING SITE FOR RESIDUE NAG G 834
08
AC8
SOFTWARE
MET G:373 , ASN G:386 , THR G:388 , HOH G:585
BINDING SITE FOR RESIDUE NAG G 886
09
AC9
SOFTWARE
GLN G:389 , ASN G:392 , CYS G:395 , MET G:407 , GLY G:409 , CYS G:410
BINDING SITE FOR RESIDUE NAG G 892
10
BC1
SOFTWARE
SER G:291 , ASN G:448 , HOH G:512 , HOH G:543 , HOH G:661
BINDING SITE FOR RESIDUE NAG G 948
11
BC2
SOFTWARE
HOH G:24 , HOH G:171 , ASN G:474 , LYS G:476 , ARG G:480 , HOH G:633 , HOH G:667 , TYR H:98
BINDING SITE FOR RESIDUE SO4 G 1000
12
BC3
SOFTWARE
ARG G:327 , ILE G:420 , LYS G:421 , GLN G:422 , ILE G:423 , HOH G:536 , GOL G:1005
BINDING SITE FOR RESIDUE SO4 G 1001
13
BC4
SOFTWARE
LYS G:290 , LYS G:340 , GLN G:344 , NAG G:789
BINDING SITE FOR RESIDUE SO4 G 1002
14
BC5
SOFTWARE
ASP G:107 , ILE G:423 , HOH G:623 , SO4 G:1001
BINDING SITE FOR RESIDUE GOL G 1005
15
BC6
SOFTWARE
ASP G:230 , LYS G:231 , PHE G:233 , GLU G:267 , ILE G:271 , ARG G:273 , TYR G:484 , LYS G:485 , HOH G:500
BINDING SITE FOR RESIDUE GOL G 1006
16
BC7
SOFTWARE
ASN G:276 , LEU G:277 , THR G:278 , HOH G:503 , NAG G:776 , CL G:1015
BINDING SITE FOR RESIDUE GOL G 1007
17
BC8
SOFTWARE
GLY G:124 , GLY G:429 , THR G:430 , GLY G:431 , ARG H:73 , ASP H:74
BINDING SITE FOR RESIDUE GOL G 1008
18
BC9
SOFTWARE
HOH G:8 , HOH G:32 , PRO G:363 , ASN G:386 , THR G:388 , HOH G:585
BINDING SITE FOR RESIDUE CL G 1013
19
CC1
SOFTWARE
ALA G:58 , HOH G:547 , HOH G:605
BINDING SITE FOR RESIDUE CL G 1014
20
CC2
SOFTWARE
LEU G:277 , NAG G:734 , GOL G:1007
BINDING SITE FOR RESIDUE CL G 1015
21
CC3
SOFTWARE
ILE G:109 , ASP G:113 , GLN G:428
BINDING SITE FOR RESIDUE CL G 1016
22
CC4
SOFTWARE
HIS G:249 , GLY G:250
BINDING SITE FOR RESIDUE CL G 1017
23
CC5
SOFTWARE
TRP G:69 , HIS G:72 , GLN G:114
BINDING SITE FOR RESIDUE CL G 1019
24
CC6
SOFTWARE
PRO G:299 , SER G:300
BINDING SITE FOR RESIDUE CL G 1022
25
CC7
SOFTWARE
ILE G:272 , LYS G:348 , HIS G:352 , HOH G:540
BINDING SITE FOR RESIDUE CL G 1027
26
CC8
SOFTWARE
MET G:434
BINDING SITE FOR RESIDUE CL G 1028
27
CC9
SOFTWARE
HOH G:163 , ASP G:368 , GLU G:370 , ASN G:425 , MET G:426 , VAL H:52B , THR H:53
BINDING SITE FOR RESIDUE BU3 G 1030
28
DC1
SOFTWARE
PRO H:61 , ASP H:62 , HOH H:356
BINDING SITE FOR RESIDUE CL H 1010
29
DC2
SOFTWARE
SER H:127 , LYS H:129 , ALA H:137 , PHE L:116
BINDING SITE FOR RESIDUE CL H 1023
30
DC3
SOFTWARE
VAL H:152
BINDING SITE FOR RESIDUE CL H 1026
31
DC4
SOFTWARE
PHE H:166 , PRO H:167 , VAL H:169 , SER H:177 , LEU H:178 , SER H:179 , GLN L:160 , SER L:162 , SER L:176 , THR L:178
BINDING SITE FOR RESIDUE TRS H 1040
32
DC5
SOFTWARE
SER L:121 , ASP L:122 , GLU L:123
BINDING SITE FOR RESIDUE SO4 L 1003
33
DC6
SOFTWARE
ARG L:85 , ARG L:142
BINDING SITE FOR RESIDUE SO4 L 1004
34
DC7
SOFTWARE
SER L:27 , TYR L:30
BINDING SITE FOR RESIDUE CL L 1011
35
DC8
SOFTWARE
LYS L:145 , GLU L:195 , THR L:197
BINDING SITE FOR RESIDUE CL L 1012
36
DC9
SOFTWARE
LYS H:143 , GLN L:124 , THR L:129
BINDING SITE FOR RESIDUE CL L 1018
37
EC1
SOFTWARE
SER L:63 , GLY L:64 , SER L:65 , THR L:72 , THR L:74
BINDING SITE FOR RESIDUE CL L 1020
38
EC2
SOFTWARE
THR L:5 , SER L:7 , SER L:22 , THR L:24
BINDING SITE FOR RESIDUE CL L 1024
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3se9l1 (L:1-107)
2a: SCOP_d3se9l2 (L:108-214)
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
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d3se9l1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d3se9l2
L:108-214
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain G
Chain H
Chain L
Asymmetric Unit 1
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Example Commands
Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (397 KB)
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