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4LAJ
Asym. Unit
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
]
Hetero Components
(7, 59)
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
4
Mod. Amino Acid
D-PROLINE
3
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
4
MPT
4
Mod. Amino Acid
BETA-MERCAPTOPROPIONIC ACID
5
NAG
35
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NH2
4
Mod. Amino Acid
AMINO GROUP
7
U2X
4
Mod. Amino Acid
O-(CYCLOHEXYLMETHYL)-L-TYROSINE
[
close Hetero Component info
]
Sites
(47, 47)
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)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS K:19 , ALA K:20 , THR K:22 , U2X K:23
BINDING SITE FOR RESIDUE DPR K 21
02
AC2
SOFTWARE
ARG A:476 , ALA D:20 , THR D:22 , U2X D:23
BINDING SITE FOR RESIDUE DPR D 21
03
AC3
SOFTWARE
ALA G:20 , THR G:22 , U2X G:23
BINDING SITE FOR RESIDUE DPR G 21
04
AC4
SOFTWARE
ALA C:20 , THR C:22 , U2X C:23
BINDING SITE FOR RESIDUE DPR C 21
05
AC5
SOFTWARE
ASN J:88
BINDING SITE FOR RESIDUE NAG J 505
06
AC6
SOFTWARE
TRP J:112 , MET J:426 , TRP J:427 , GLN J:428 , TYR J:435
BINDING SITE FOR RESIDUE EDO J 510
07
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
08
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
09
AC9
SOFTWARE
MET A:426 , TRP A:427 , GLN A:428 , TYR A:435 , HOH A:706
BINDING SITE FOR RESIDUE EDO A 510
10
BC1
SOFTWARE
ASP A:62 , GLU A:64 , GLU A:211 , ARG B:440
BINDING SITE FOR RESIDUE EDO A 511
11
BC2
SOFTWARE
PHE A:210 , GLY A:379 , ILE A:439 , HOH A:713
BINDING SITE FOR RESIDUE EDO A 512
12
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
13
BC4
SOFTWARE
MET B:426 , TRP B:427 , GLN B:428 , TYR B:435
BINDING SITE FOR RESIDUE EDO B 509
14
BC5
SOFTWARE
LEU B:116 , LYS B:117 , PRO B:206 , GLY B:380 , TYR B:435 , HOH B:622
BINDING SITE FOR RESIDUE EDO B 510
15
BC6
SOFTWARE
SER B:446 , ASN B:448 , NAG B:508
BINDING SITE FOR RESIDUE EDO B 511
16
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
17
BC8
SOFTWARE
ASN A:234 , THR A:236 , SER A:274
BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 234
18
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
19
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
20
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
21
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
22
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
23
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
24
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
25
CC7
SOFTWARE
ASN B:234 , THR B:236 , PRO B:238 , SER B:274
BINDING SITE FOR MONO-SACCHARIDE NAG B 503 BOUND TO ASN B 234
26
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
27
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
28
DC1
SOFTWARE
GLU B:268 , GLU B:269 , ILE B:270 , ASN B:289 , GLU B:290 , GLN B:344 , HOH B:666 , SER H:63
BINDING SITE FOR MONO-SACCHARIDE NAG B 505 BOUND TO ASN B 289
29
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
30
DC3
SOFTWARE
VAL B:372 , ASN B:386 , THR B:388 , HOH B:619 , HOH B:694 , HOH B:728 , GLU I:44 , SER I:106 , LEU I:107 , LEU I:108 , TYR I:109 , HOH I:208
BINDING SITE FOR MONO-SACCHARIDE NAG B 507 BOUND TO ASN B 386
31
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
32
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
33
DC6
SOFTWARE
ASN F:229 , LYS F:231 , ASN F:241
BINDING SITE FOR MONO-SACCHARIDE NAG F 503 BOUND TO ASN F 241
34
DC7
SOFTWARE
GLU F:211 , PRO F:212 , LEU F:261 , ASN F:262 , CYS F:445 , SER F:446 , SER F:447 , NAG F:508 , HOH F:606 , HOH F:660 , HOH F:709 , HOH J:614
BINDING SITE FOR MONO-SACCHARIDE NAG F 504 BOUND TO ASN F 262
35
DC8
SOFTWARE
ASN F:276 , THR F:278 , ASN F:279
BINDING SITE FOR MONO-SACCHARIDE NAG F 501 BOUND TO ASN F 276
36
DC9
SOFTWARE
GLU F:268 , GLU F:269 , ILE F:270 , ASN F:289 , GLU F:290 , GLN F:344 , HOH F:649
BINDING SITE FOR MONO-SACCHARIDE NAG F 505 BOUND TO ASN F 289
37
EC1
SOFTWARE
ASN F:295 , LEU F:333 , SER F:334 , ARG F:444 , SER F:446
BINDING SITE FOR MONO-SACCHARIDE NAG F 506 BOUND TO ASN F 295
38
EC2
SOFTWARE
ASN F:386 , THR F:388 , GLU M:44 , SER M:106 , LEU M:107 , LEU M:108 , TYR M:109
BINDING SITE FOR MONO-SACCHARIDE NAG F 507 BOUND TO ASN F 386
39
EC3
SOFTWARE
ARG F:252 , ASN F:262 , SER F:291 , ASN F:448 , NAG F:504 , HOH F:619 , HOH F:640 , HOH F:694 , ASN J:301
BINDING SITE FOR MONO-SACCHARIDE NAG F 508 BOUND TO ASN F 448
40
EC4
SOFTWARE
ASN J:234 , THR J:236 , PRO J:238 , SER J:274
BINDING SITE FOR MONO-SACCHARIDE NAG J 502 BOUND TO ASN J 234
41
EC5
SOFTWARE
LYS J:85 , GLU J:87 , ASN J:229 , ASN J:241
BINDING SITE FOR MONO-SACCHARIDE NAG J 503 BOUND TO ASN J 241
42
EC6
SOFTWARE
ASN F:300 , GLU J:211 , PRO J:212 , ARG J:252 , LEU J:261 , ASN J:262 , CYS J:445 , SER J:446 , SER J:447 , NAG J:509 , HOH J:607 , HOH J:612
BINDING SITE FOR MONO-SACCHARIDE NAG J 504 BOUND TO ASN J 262
43
EC7
SOFTWARE
ASN J:276 , THR J:278 , ASN J:279 , SER M:124
BINDING SITE FOR MONO-SACCHARIDE NAG J 501 BOUND TO ASN J 276
44
EC8
SOFTWARE
GLU J:269 , ILE J:270 , ASN J:289 , GLU J:290 , GLN J:344
BINDING SITE FOR MONO-SACCHARIDE NAG J 506 BOUND TO ASN J 289
45
EC9
SOFTWARE
ASN J:295 , ASN J:413 , ARG J:444 , HOH J:640
BINDING SITE FOR MONO-SACCHARIDE NAG J 507 BOUND TO ASN J 295
46
FC1
SOFTWARE
GLU H:44 , SER H:106 , LEU H:107 , LEU H:108 , TYR H:109 , ASN J:386 , THR J:388 , HOH J:669
BINDING SITE FOR MONO-SACCHARIDE NAG J 508 BOUND TO ASN J 386
47
FC2
SOFTWARE
ASN F:301 , SER J:291 , ASN J:448 , NAG J:504
BINDING SITE FOR MONO-SACCHARIDE NAG J 509 BOUND TO ASN J 448
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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CATH Domains
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Pfam Domains
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