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4J6R
Asym. Unit
Info
Asym.Unit (410 KB)
Biol.Unit 1 (399 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BROADLY AND POTENTLY NEUTRALIZING ANTIBODY VRC23 IN COMPLEX WITH HIV-1 GP120
Authors
:
T. Zhou, S. Moquin, Kwong P. D.
Date
:
11 Feb 13 (Deposition) - 08 May 13 (Release) - 29 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.64
Chains
:
Asym. Unit : G,H,L
Biol. Unit 1: G,H,L (1x)
Keywords
:
Hiv, Gp120, Cd4-Binding Site, Vrc23, Neutralization, Vaccine, Antibody, Envelope Protein, Immune System, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. S. Georgiev, N. A. Doria-Rose, T. Zhou, Y. D. Kwon, R. P. Staupe, S. Moquin, G. Y. Chuang, M. K. Louder, S. D. Schmidt, H. R. Altae-Tran, R. T. Bailer, K. Mckee, M. Nason, S. O'Dell, G. Ofek, M. Pancera, S. Srivatsan, L. Shapiro, M. Connors, S. A. Migueles, L. Morris, Y. Nishimura, M. A. Martin, J. R. Mascola, P. D. Kwong
Delineating Antibody Recognition In Polyclonal Sera From Patterns Of Hiv-1 Isolate Neutralization.
Science V. 340 751 2013
[
close entry info
]
Hetero Components
(7, 30)
Info
All Hetero Components
1a: (R,R)-2,3-BUTANEDIOL (BU3a)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
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)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6a: PYROGLUTAMIC ACID (PCAa)
7a: 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
CA
2
Ligand/Ion
CALCIUM ION
3
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
4
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
PCA
1
Mod. Amino Acid
PYROGLUTAMIC ACID
7
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE G:233 , ASN G:234 , THR G:236 , LEU G:238 , HOH G:718 , HOH G:820
BINDING SITE FOR RESIDUE NAG G 501
02
AC2
SOFTWARE
ASP G:230 , GLU G:231 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 502
03
AC3
SOFTWARE
GLU G:211 , PRO G:212 , ASN G:262 , GLU G:446 , SER G:447 , HOH G:619 , HOH G:658 , HOH G:738 , HOH G:799
BINDING SITE FOR RESIDUE NAG G 503
04
AC4
SOFTWARE
ASN G:276 , THR G:278 , VAL L:29 , GLY L:30 , ASP L:32 , GLN L:90 , TYR L:91 , HOH L:513
BINDING SITE FOR RESIDUE NAG G 504
05
AC5
SOFTWARE
LYS G:295 , HIS G:330 , ASN G:332 , HOH G:828 , HOH G:835 , HOH G:881
BINDING SITE FOR RESIDUE NAG G 505
06
AC6
SOFTWARE
LYS G:117 , ASN G:363 , THR G:372 , ASN G:386 , SER G:388 , NAG G:507 , HOH G:687 , HOH G:782 , HOH G:797 , HOH G:832 , HOH G:909
BINDING SITE FOR RESIDUE NAG G 506
07
AC7
SOFTWARE
LYS G:117 , ASN G:386 , SER G:388 , NAG G:506 , HOH G:676 , HOH G:677 , HOH G:743 , HOH G:782
BINDING SITE FOR RESIDUE NAG G 507
08
AC8
SOFTWARE
ASN G:392 , HOH G:740
BINDING SITE FOR RESIDUE NAG G 508
09
AC9
SOFTWARE
LEU G:265 , PRO G:291 , GLU G:446 , ASN G:448 , HOH G:683
BINDING SITE FOR RESIDUE NAG G 509
10
BC1
SOFTWARE
LYS G:421 , GLN G:422 , ILE G:423
BINDING SITE FOR RESIDUE CA G 510
11
BC2
SOFTWARE
ASN G:234 , ILE G:272 , ARG G:273 , SER G:274 , TYR G:352 , HOH G:667 , HOH G:724 , HOH G:918
BINDING SITE FOR RESIDUE EDO G 511
12
BC3
SOFTWARE
GLY G:250 , LYS G:252 , ASN G:262 , GLY G:263 , HOH G:672 , HOH G:826
BINDING SITE FOR RESIDUE EDO G 512
13
BC4
SOFTWARE
VAL G:254 , LEU G:261 , GLY G:263 , ASN G:478 , HOH G:613 , HOH G:645 , HOH G:672
BINDING SITE FOR RESIDUE EDO G 513
14
BC5
SOFTWARE
THR G:400 , ASP G:403
BINDING SITE FOR RESIDUE EDO G 514
15
BC6
SOFTWARE
GLU H:23 , THR H:75 , HOH H:462 , HOH H:505
BINDING SITE FOR RESIDUE MPD H 301
16
BC7
SOFTWARE
SER H:7 , ARG H:19 , SER H:21
BINDING SITE FOR RESIDUE EDO H 302
17
BC8
SOFTWARE
GLU H:148 , PRO H:149 , VAL H:150 , ALA H:168 , HOH H:621
BINDING SITE FOR RESIDUE EDO H 303
18
BC9
SOFTWARE
TYR H:32 , ARG H:94 , VAL H:96 , PHE H:102 , HOH H:616
BINDING SITE FOR RESIDUE EDO H 304
19
CC1
SOFTWARE
ALA H:9 , PRO H:149 , HOH H:481 , HOH H:594 , HOH H:725
BINDING SITE FOR RESIDUE EDO H 305
20
CC2
SOFTWARE
LEU H:141 , VAL H:169 , SER H:177 , LEU H:178 , SER H:179 , HOH H:420 , THR L:178 , HOH L:412 , HOH L:413
BINDING SITE FOR RESIDUE EDO H 306
21
CC3
SOFTWARE
LYS H:13 , ALA H:114 , SER H:115 , THR H:116 , HOH H:426 , HOH H:655
BINDING SITE FOR RESIDUE EDO H 307
22
CC4
SOFTWARE
THR H:151 , SER H:153 , ASN H:197 , HOH H:658 , HOH H:679
BINDING SITE FOR RESIDUE EDO H 308
23
CC5
SOFTWARE
GLN H:105 , GLY H:106 , HOH H:617 , HOH H:654 , HOH H:681 , HOH H:717
BINDING SITE FOR RESIDUE EDO H 309
24
CC6
SOFTWARE
SER H:161 , GLY H:162 , HOH H:456 , HOH H:592 , HOH H:732 , SER L:65 , GLY L:66 , ASP L:167 , ASP L:170 , HOH L:453
BINDING SITE FOR RESIDUE TRS H 310
25
CC7
SOFTWARE
ARG L:15 , HIS L:68 , HOH L:540 , HOH L:743
BINDING SITE FOR RESIDUE CA L 301
26
CC8
SOFTWARE
ARG H:44 , MET L:4 , GLN L:100 , HOH L:415
BINDING SITE FOR RESIDUE EDO L 302
27
CC9
SOFTWARE
LYS L:39 , PRO L:80 , GLU L:81 , VAL L:83 , HOH L:583 , HOH L:629
BINDING SITE FOR RESIDUE EDO L 303
28
DC1
SOFTWARE
LYS L:107 , BU3 L:305 , HOH L:582
BINDING SITE FOR RESIDUE EDO L 304
29
DC2
SOFTWARE
ARG L:108 , THR L:109 , EDO L:304 , HOH L:537
BINDING SITE FOR RESIDUE BU3 L 305
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d4j6rl1 (L:1-107)
2a: SCOP_d4j6rl2 (L:108-214)
View:
Select:
Label:
Classes
(
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(
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Folds
(
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(
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Superfamilies
(
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(
)
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
d4j6rl1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d4j6rl2
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
[
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]
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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select residue range 5 to 10 in chain 'A'
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set label size to 20 (allowed range: 1-58)
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