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4LAJ
Biol. Unit 3
Info
Asym.Unit (709 KB)
Biol.Unit 1 (179 KB)
Biol.Unit 2 (178 KB)
Biol.Unit 3 (182 KB)
Biol.Unit 4 (182 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 YU2 ENVELOPE GP120 GLYCOPROTEIN IN COMPLEX WITH CD4-MIMETIC MINIPROTEIN, M48U1, AND LLAMA SINGLE-DOMAIN, BROADLY NEUTRALIZING, CO-RECEPTOR BINDING SITE ANTIBODY, JM4
Authors
:
P. Acharya, T. S. Luongo, P. D. Kwong
Date
:
20 Jun 13 (Deposition) - 14 Aug 13 (Release) - 09 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.14
Chains
:
Asym. Unit : A,B,C,D,F,G,H,I,J,K,L,M
Biol. Unit 1: H,J,K (1x)
Biol. Unit 2: F,G,M (1x)
Biol. Unit 3: A,D,L (1x)
Biol. Unit 4: B,C,I (1x)
Keywords
:
Cd4-Induced Antibody, Hiv-1 Neutralizing Antibody, Hiv-1 Gp120 Reactive, Viral Protein-Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Acharya, T. S. Luongo, I. S. Georgiev, J. Matz, S. D. Schmidt, M. K. Louder, P. Kessler, Y. Yang, K. Mckee, S. O'Dell, L. Chen, D. Baty, P. Chames, L. Martin, J. R. Mascola, P. D. Kwong
Heavy Chain-Only Igg2B Llama Antibody Effects Near-Pan Hiv- Neutralization By Recognizing A Cd4-Induced Epitope That Includes Elements Of Coreceptor- And Cd4-Binding Sites.
J. Virol. V. 87 10173 2013
[
close entry info
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Hetero Components
(6, 16)
Info
All Hetero Components
1a: 6-AMINOHEXANOIC ACID (ACAa)
2a: D-PROLINE (DPRa)
2b: D-PROLINE (DPRb)
2c: D-PROLINE (DPRc)
2d: D-PROLINE (DPRd)
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)
4a: BETA-MERCAPTOPROPIONIC ACID (MPTa)
4b: BETA-MERCAPTOPROPIONIC ACID (MPTb)
4c: BETA-MERCAPTOPROPIONIC ACID (MPTc)
4d: BETA-MERCAPTOPROPIONIC ACID (MPTd)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
5ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
5ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
5ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
5ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
5af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
5ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
5ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
5ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
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)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
5o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5p: N-ACETYL-D-GLUCOSAMINE (NAGp)
5q: N-ACETYL-D-GLUCOSAMINE (NAGq)
5r: N-ACETYL-D-GLUCOSAMINE (NAGr)
5s: N-ACETYL-D-GLUCOSAMINE (NAGs)
5t: N-ACETYL-D-GLUCOSAMINE (NAGt)
5u: N-ACETYL-D-GLUCOSAMINE (NAGu)
5v: N-ACETYL-D-GLUCOSAMINE (NAGv)
5w: N-ACETYL-D-GLUCOSAMINE (NAGw)
5x: N-ACETYL-D-GLUCOSAMINE (NAGx)
5y: N-ACETYL-D-GLUCOSAMINE (NAGy)
5z: N-ACETYL-D-GLUCOSAMINE (NAGz)
6a: AMINO GROUP (NH2a)
6b: AMINO GROUP (NH2b)
6c: AMINO GROUP (NH2c)
6d: AMINO GROUP (NH2d)
7a: O-(CYCLOHEXYLMETHYL)-L-TYROSINE (U2Xa)
7b: O-(CYCLOHEXYLMETHYL)-L-TYROSINE (U2Xb)
7c: O-(CYCLOHEXYLMETHYL)-L-TYROSINE (U2Xc)
7d: O-(CYCLOHEXYLMETHYL)-L-TYROSINE (U2Xd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACA
-1
Ligand/Ion
6-AMINOHEXANOIC ACID
2
DPR
1
Mod. Amino Acid
D-PROLINE
3
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
4
MPT
1
Mod. Amino Acid
BETA-MERCAPTOPROPIONIC ACID
5
NAG
9
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NH2
1
Mod. Amino Acid
AMINO GROUP
7
U2X
1
Mod. Amino Acid
O-(CYCLOHEXYLMETHYL)-L-TYROSINE
[
close Hetero Component info
]
Sites
(21, 21)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC8 (SOFTWARE)
18: CC9 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC4 (SOFTWARE)
21: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
ARG A:476 , ALA D:20 , THR D:22 , U2X D:23
BINDING SITE FOR RESIDUE DPR D 21
02
AC7
SOFTWARE
THR A:396 , LEU A:399 , ASN A:400 , ASP F:230 , LYS F:232 , PHE F:233 , ASN F:234 , THR F:240 , NAG F:502 , HOH F:683
BINDING SITE FOR RESIDUE NAG F 509
03
AC8
SOFTWARE
ASN A:295 , THR A:297 , HIS A:330 , ASN A:332 , ARG A:444 , NAG A:506 , NAG B:506
BINDING SITE FOR RESIDUE NAG A 502
04
AC9
SOFTWARE
MET A:426 , TRP A:427 , GLN A:428 , TYR A:435 , HOH A:706
BINDING SITE FOR RESIDUE EDO A 510
05
BC1
SOFTWARE
ASP A:62 , GLU A:64 , GLU A:211 , ARG B:440
BINDING SITE FOR RESIDUE EDO A 511
06
BC2
SOFTWARE
PHE A:210 , GLY A:379 , ILE A:439 , HOH A:713
BINDING SITE FOR RESIDUE EDO A 512
07
BC3
SOFTWARE
NAG A:506 , ASN B:295 , HIS B:330 , ASN B:332 , ARG B:444 , NAG B:506
BINDING SITE FOR RESIDUE NAG B 502
08
BC7
SOFTWARE
ASN A:300 , ARG A:440 , GLY A:441 , ASP B:57 , PRO B:214 , HIS B:216 , ARG B:252
BINDING SITE FOR RESIDUE ACA B 512
09
BC8
SOFTWARE
ASN A:234 , THR A:236 , SER A:274
BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 234
10
BC9
SOFTWARE
GLU A:211 , PRO A:212 , LEU A:261 , ASN A:262 , CYS A:445 , SER A:447 , NAG A:509 , HOH A:604 , HOH A:605 , HOH A:710 , HOH A:714 , ASN B:300
BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 262
11
CC1
SOFTWARE
ASN A:276 , THR A:278 , ASN A:279 , PRO I:41
BINDING SITE FOR MONO-SACCHARIDE NAG A 501 BOUND TO ASN A 276
12
CC2
SOFTWARE
GLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:290 , GLN A:344 , HOH A:640
BINDING SITE FOR MONO-SACCHARIDE NAG A 505 BOUND TO ASN A 289
13
CC3
SOFTWARE
ASN A:295 , LEU A:333 , ASN A:413 , ARG A:444 , NAG A:502 , HOH A:707 , NAG B:502
BINDING SITE FOR MONO-SACCHARIDE NAG A 506 BOUND TO ASN A 295
14
CC4
SOFTWARE
VAL A:372 , ASN A:386 , THR A:388 , HOH A:610 , SER L:106 , LEU L:107 , LEU L:108 , TYR L:109
BINDING SITE FOR MONO-SACCHARIDE NAG A 507 BOUND TO ASN A 386
15
CC5
SOFTWARE
THR A:392 , ASN A:394 , THR A:396 , LYS F:232 , GLU F:268
BINDING SITE FOR MONO-SACCHARIDE NAG A 508 BOUND TO ASN A 394
16
CC6
SOFTWARE
SER A:291 , ASN A:448 , NAG A:504 , HOH A:647 , HOH A:661
BINDING SITE FOR MONO-SACCHARIDE NAG A 509 BOUND TO ASN A 448
17
CC8
SOFTWARE
ASN A:300 , GLU B:211 , PRO B:212 , ARG B:252 , LEU B:261 , ASN B:262 , CYS B:445 , SER B:446 , SER B:447 , NAG B:508 , HOH B:610 , HOH B:612 , HOH B:690 , HOH B:739
BINDING SITE FOR MONO-SACCHARIDE NAG B 504 BOUND TO ASN B 262
18
CC9
SOFTWARE
ASN B:276 , THR B:278 , ASN B:279 , HOH B:720 , PRO L:41
BINDING SITE FOR MONO-SACCHARIDE NAG B 501 BOUND TO ASN B 276
19
DC2
SOFTWARE
NAG A:502 , ASN B:295 , ARG B:444 , SER B:446 , NAG B:502 , HOH B:685
BINDING SITE FOR MONO-SACCHARIDE NAG B 506 BOUND TO ASN B 295
20
DC4
SOFTWARE
ASN A:300 , ASN A:301 , ARG B:252 , SER B:291 , ASN B:448 , NAG B:504 , EDO B:511 , HOH B:638 , HOH B:641
BINDING SITE FOR MONO-SACCHARIDE NAG B 508 BOUND TO ASN B 448
21
DC5
SOFTWARE
LEU A:399 , ASN F:234 , THR F:236 , SER F:274 , NAG F:509 , HOH F:622 , HOH F:704
BINDING SITE FOR MONO-SACCHARIDE NAG F 502 BOUND TO ASN F 234
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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[
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Exons
(0, 0)
Info
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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
(0, 0)
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CATH Domains
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all CATH domains
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Pfam Domains
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Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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