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5FYJ
Asym. Unit
Info
Asym.Unit (665 KB)
Biol.Unit 1, α-C (1.8 MB)
Biol.Unit 1 (1.8 MB)
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(1)
Title
:
CRYSTAL STRUCTURE AT 3.4 A RESOLUTION OF FULLY GLYCOSYLATED HIV-1 CLADE G X1193.C1 SOSIP.664 PREFUSION ENV TRIMER IN COMPLEX WITH BROADLY NEUTRALIZING ANTIBODIES PGT122, 35O22 AND VRC01
Authors
:
G. B. E. Stewart-Jones, T. Zhou, P. V. Thomas, P. D. Kwong
Date
:
08 Mar 16 (Deposition) - 27 Apr 16 (Release) - 12 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.11
Chains
:
Asym. Unit : B,D,E,G,H,L,U,V
Biol. Unit 1: B,D,E,G,H,L,U,V (3x)
Keywords
:
Viral Protein, Hiv, Envelope, Glycan, Trimer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. B. E. Stewart-Jones, C. Soto, T. Lemmin, G. Y. Chuang, A. Druz, R. Kong, P. V. Thomas, K. Wagh, T. Zhou, A. J. Behrens, T. Bylund, C. W. Choi, J. R. Davison, I. S. Georgiev, M. G. Joyce, Y. D. Kwon, M. Pancera, J. Taft, Y. Yang, B. Zhang, S. S. Shivatare, V. S. Shivatare C. C. D. Lee, C. Y. Wu, C. A. Bewley, D. R. Burton, W. C. Koff, M. Connors, M. Crispin, B. T. Korber, C. H. Wong, J. R. Mascola, P. D. Kwong
Trimeric Hiv-1-Env Structures Define Glycan Shields From Clades A, B And G
Cell(Cambridge, Mass. ) V. 165 813 2016
[
close entry info
]
Hetero Components
(5, 167)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
1h: BETA-D-MANNOSE (BMAh)
1i: BETA-D-MANNOSE (BMAi)
1j: BETA-D-MANNOSE (BMAj)
1k: BETA-D-MANNOSE (BMAk)
1l: BETA-D-MANNOSE (BMAl)
1m: BETA-D-MANNOSE (BMAm)
1n: BETA-D-MANNOSE (BMAn)
1o: BETA-D-MANNOSE (BMAo)
1p: BETA-D-MANNOSE (BMAp)
1q: BETA-D-MANNOSE (BMAq)
1r: BETA-D-MANNOSE (BMAr)
1s: BETA-D-MANNOSE (BMAs)
1t: BETA-D-MANNOSE (BMAt)
2a: CITRIC ACID (CITa)
2b: CITRIC ACID (CITb)
2c: CITRIC ACID (CITc)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
4a: ALPHA-D-MANNOSE (MANa)
4aa: ALPHA-D-MANNOSE (MANaa)
4ab: ALPHA-D-MANNOSE (MANab)
4ac: ALPHA-D-MANNOSE (MANac)
4ad: ALPHA-D-MANNOSE (MANad)
4ae: ALPHA-D-MANNOSE (MANae)
4af: ALPHA-D-MANNOSE (MANaf)
4ag: ALPHA-D-MANNOSE (MANag)
4ah: ALPHA-D-MANNOSE (MANah)
4ai: ALPHA-D-MANNOSE (MANai)
4aj: ALPHA-D-MANNOSE (MANaj)
4ak: ALPHA-D-MANNOSE (MANak)
4al: ALPHA-D-MANNOSE (MANal)
4am: ALPHA-D-MANNOSE (MANam)
4an: ALPHA-D-MANNOSE (MANan)
4ao: ALPHA-D-MANNOSE (MANao)
4ap: ALPHA-D-MANNOSE (MANap)
4aq: ALPHA-D-MANNOSE (MANaq)
4ar: ALPHA-D-MANNOSE (MANar)
4as: ALPHA-D-MANNOSE (MANas)
4at: ALPHA-D-MANNOSE (MANat)
4au: ALPHA-D-MANNOSE (MANau)
4av: ALPHA-D-MANNOSE (MANav)
4aw: ALPHA-D-MANNOSE (MANaw)
4ax: ALPHA-D-MANNOSE (MANax)
4ay: ALPHA-D-MANNOSE (MANay)
4az: ALPHA-D-MANNOSE (MANaz)
4b: ALPHA-D-MANNOSE (MANb)
4ba: ALPHA-D-MANNOSE (MANba)
4bb: ALPHA-D-MANNOSE (MANbb)
4bc: ALPHA-D-MANNOSE (MANbc)
4bd: ALPHA-D-MANNOSE (MANbd)
4be: ALPHA-D-MANNOSE (MANbe)
4bf: ALPHA-D-MANNOSE (MANbf)
4bg: ALPHA-D-MANNOSE (MANbg)
4bh: ALPHA-D-MANNOSE (MANbh)
4bi: ALPHA-D-MANNOSE (MANbi)
4bj: ALPHA-D-MANNOSE (MANbj)
4bk: ALPHA-D-MANNOSE (MANbk)
4bl: ALPHA-D-MANNOSE (MANbl)
4bm: ALPHA-D-MANNOSE (MANbm)
4bn: ALPHA-D-MANNOSE (MANbn)
4bo: ALPHA-D-MANNOSE (MANbo)
4bp: ALPHA-D-MANNOSE (MANbp)
4bq: ALPHA-D-MANNOSE (MANbq)
4br: ALPHA-D-MANNOSE (MANbr)
4bs: ALPHA-D-MANNOSE (MANbs)
4bt: ALPHA-D-MANNOSE (MANbt)
4bu: ALPHA-D-MANNOSE (MANbu)
4bv: ALPHA-D-MANNOSE (MANbv)
4bw: ALPHA-D-MANNOSE (MANbw)
4bx: ALPHA-D-MANNOSE (MANbx)
4by: ALPHA-D-MANNOSE (MANby)
4bz: ALPHA-D-MANNOSE (MANbz)
4c: ALPHA-D-MANNOSE (MANc)
4ca: ALPHA-D-MANNOSE (MANca)
4cb: ALPHA-D-MANNOSE (MANcb)
4cc: ALPHA-D-MANNOSE (MANcc)
4cd: ALPHA-D-MANNOSE (MANcd)
4ce: ALPHA-D-MANNOSE (MANce)
4cf: ALPHA-D-MANNOSE (MANcf)
4cg: ALPHA-D-MANNOSE (MANcg)
4ch: ALPHA-D-MANNOSE (MANch)
4ci: ALPHA-D-MANNOSE (MANci)
4cj: ALPHA-D-MANNOSE (MANcj)
4ck: ALPHA-D-MANNOSE (MANck)
4cl: ALPHA-D-MANNOSE (MANcl)
4cm: ALPHA-D-MANNOSE (MANcm)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
4g: ALPHA-D-MANNOSE (MANg)
4h: ALPHA-D-MANNOSE (MANh)
4i: ALPHA-D-MANNOSE (MANi)
4j: ALPHA-D-MANNOSE (MANj)
4k: ALPHA-D-MANNOSE (MANk)
4l: ALPHA-D-MANNOSE (MANl)
4m: ALPHA-D-MANNOSE (MANm)
4n: ALPHA-D-MANNOSE (MANn)
4o: ALPHA-D-MANNOSE (MANo)
4p: ALPHA-D-MANNOSE (MANp)
4q: ALPHA-D-MANNOSE (MANq)
4r: ALPHA-D-MANNOSE (MANr)
4s: ALPHA-D-MANNOSE (MANs)
4t: ALPHA-D-MANNOSE (MANt)
4u: ALPHA-D-MANNOSE (MANu)
4v: ALPHA-D-MANNOSE (MANv)
4w: ALPHA-D-MANNOSE (MANw)
4x: ALPHA-D-MANNOSE (MANx)
4y: ALPHA-D-MANNOSE (MANy)
4z: ALPHA-D-MANNOSE (MANz)
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)
5aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
5ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
5al: N-ACETYL-D-GLUCOSAMINE (NAGal)
5am: N-ACETYL-D-GLUCOSAMINE (NAGam)
5an: N-ACETYL-D-GLUCOSAMINE (NAGan)
5ao: N-ACETYL-D-GLUCOSAMINE (NAGao)
5ap: N-ACETYL-D-GLUCOSAMINE (NAGap)
5aq: N-ACETYL-D-GLUCOSAMINE (NAGaq)
5ar: N-ACETYL-D-GLUCOSAMINE (NAGar)
5as: N-ACETYL-D-GLUCOSAMINE (NAGas)
5at: N-ACETYL-D-GLUCOSAMINE (NAGat)
5au: N-ACETYL-D-GLUCOSAMINE (NAGau)
5av: N-ACETYL-D-GLUCOSAMINE (NAGav)
5aw: N-ACETYL-D-GLUCOSAMINE (NAGaw)
5ax: N-ACETYL-D-GLUCOSAMINE (NAGax)
5ay: N-ACETYL-D-GLUCOSAMINE (NAGay)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
20
Ligand/Ion
BETA-D-MANNOSE
2
CIT
3
Ligand/Ion
CITRIC ACID
3
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
4
MAN
91
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
51
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(33, 33)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:585 , GLN B:588 , ASP B:589 , LYS G:492
BINDING SITE FOR RESIDUE CIT B 1666
02
AC2
SOFTWARE
ARG B:633 , THR D:72F , SER D:72G
BINDING SITE FOR RESIDUE EDO D 1225
03
AC3
SOFTWARE
GLU G:275 , ALA G:281 , LYS G:282 , ASP G:477 , ARG G:480 , LYS U:52 , ASP U:99
BINDING SITE FOR RESIDUE CIT G 1511
04
AC4
SOFTWARE
ASP G:57 , HIS G:216
BINDING SITE FOR RESIDUE EDO G 1512
05
AC5
SOFTWARE
HIS G:105 , TRP G:427 , VAL G:430 , ASP G:474 , ARG G:476 , ARG U:53
BINDING SITE FOR RESIDUE CIT G 1513
06
AC6
SOFTWARE
MAN G:4135 , MAN G:4138
BINDING SITE FOR RESIDUE MAN G 4140B
07
AC7
SOFTWARE
ASN B:611 , SER B:613 , CYS D:216 , ASP D:217 , LYS E:186 , PRO E:208
Binding site for Poly-Saccharide residues NAG B6111 through NAG B6112 bound to ASN B 611
08
AC8
SOFTWARE
ASN B:616 , GLU B:621 , BMA B:6253 , GLY E:57
Binding site for Poly-Saccharide residues NAG B6161 through NAG B6162 bound to ASN B 616
09
AC9
SOFTWARE
GLU B:621 , ASN B:625 , LEU B:626 , GLU B:630 , GLU B:634 , NAG B:6161 , NAG B:6162 , GLN D:1 , LEU D:96 , PRO E:56
Binding site for Poly-Saccharide residues NAG B6251 through BMA B6253 bound to ASN B 625
10
BC1
SOFTWARE
ARG B:633 , ASN B:637
Binding site for Poly-Saccharide residues NAG B6371 through NAG B6372 bound to ASN B 637
11
BC2
SOFTWARE
SER B:528 , ASN D:30 , PHE D:31 , HIS D:33 , TRP D:50 , SER D:52 , TYR D:53 , ASP D:56 , ARG D:98 , ASP D:99 , GLY D:100 , SER D:100A , HOH D:2001 , HIS E:93 , ASN E:94 , ASN G:88
Binding site for Poly-Saccharide residues NAG G 881 through MAN G 888 bound to ASN G 88
12
BC3
SOFTWARE
ASN G:133 , GLN G:153 , LYS G:155 , ARG G:178
Binding site for Mono-Saccharide NAG G1331 bound to ASN G 133
13
BC4
SOFTWARE
ASN G:142 , MAN G:3869B
Binding site for Mono-Saccharide NAG G1421 bound to ASN G 142
14
BC5
SOFTWARE
VAL G:134 , ASN G:156 , TYR G:173 , GLU L:26
Binding site for Poly-Saccharide residues NAG G1561 through MAN G1569 bound to ASN G 156
15
BC6
SOFTWARE
THR G:128 , ASN G:160 , LYS G:171 , LYS G:187B , MAN G:1889A
Binding site for Poly-Saccharide residues NAG G1601 through MAN G1609 bound to ASN G 160
16
BC7
SOFTWARE
ASN G:188 , MAN G:1609
Binding site for Poly-Saccharide residues NAG G1881 through MAN G1889 bound to ASN G 188
17
BC8
SOFTWARE
ARG G:192 , ASN G:197 , ARG G:308
Binding site for Poly-Saccharide residues NAG G1971 through BMA G1973 bound to ASN G 197
18
BC9
SOFTWARE
ASN G:234 , MAN G:2766 , MAN G:2769
Binding site for Poly-Saccharide residues NAG G2341 through MAN G2346 bound to ASN G 234
19
CC1
SOFTWARE
ARG G:229 , LYS G:231 , ASN G:241 , MAN G:2937
Binding site for Poly-Saccharide residues NAG G2411 through MAN G2417 bound to ASN G 241
20
CC2
SOFTWARE
SER G:65 , PRO G:206 , LYS G:207 , VAL G:208 , THR G:209 , ASP G:211 , PRO G:212 , VAL G:254 , ASN G:262 , ARG G:304 , ARG G:379 , CYS G:445 , ARG G:446 , SER G:447 , NAG G:4421 , NAG G:4422
Binding site for Poly-Saccharide residues NAG G2621 through MAN G2629 bound to ASN G 262
21
CC3
SOFTWARE
ASN G:276 , MAN G:2344 , MAN G:2346 , TYR V:28 , GLY V:29 , SER V:30 , ARG V:66 , TRP V:67
Binding site for Poly-Saccharide residues NAG G2761 through MAN G2769 bound to ASN G 276
22
CC4
SOFTWARE
ALA G:291 , ASN G:293 , GLU G:337 , ARG G:446 , MAN G:2417 , MAN G:3444 , MAN G:4139A
Binding site for Poly-Saccharide residues NAG G2931 through MAN G2939A bound to ASN G 293
23
CC5
SOFTWARE
ASN G:301 , ILE G:323
Binding site for Poly-Saccharide residues NAG G3011 through MAN G3018 bound to ASN G 301
24
CC6
SOFTWARE
HIS G:330 , ASN G:332 , ASN G:413 , THR G:415 , NAG G:4131 , MAN G:4424 , ARG H:100 , ILE H:100A , TYR H:100B , GLY H:100C , VAL H:100D , VAL H:100E , SER L:30 , ASN L:50 , ASN L:51 , PRO L:66 , GLY L:67 , SER L:67A
Binding site for Poly-Saccharide residues NAG G3321 through MAN G3329 bound to ASN G 332
25
CC7
SOFTWARE
THR G:290 , GLU G:337 , ASP G:340 , MET G:341 , ASN G:344 , MAN G:2937 , BMA G:3553
Binding site for Poly-Saccharide residues NAG G3441 through MAN G3449A bound to ASN G 344
26
CC8
SOFTWARE
ASN G:355 , MAN G:3449A , NAG G:4642A
Binding site for Poly-Saccharide residues NAG G3551 through BMA G3553 bound to ASN G 355
27
CC9
SOFTWARE
ASN G:142 , ASP G:149 , TYR G:150 , ASN G:386 , NAG G:1421 , GLY U:65
Binding site for Poly-Saccharide residues NAG G3861 through MAN G3869A bound to ASN G 386
28
DC1
SOFTWARE
GLY G:389 , ASN G:392 , SER G:394 , THR G:415
Binding site for Mono-Saccharide NAG G3921 bound to ASN G 392
29
DC2
SOFTWARE
THR G:295 , ASN G:332 , ASN G:413 , MAN G:2936 , NAG G:3321 , MAN G:4140B , NAG G:4422
Binding site for Poly-Saccharide residues NAG G4131 through MAN G4139A bound to ASN G 413
30
DC3
SOFTWARE
ASN G:442 , MAN G:2628 , MAN G:2629B , MAN G:3329 , MAN G:4138
Binding site for Poly-Saccharide residues NAG G4421 through MAN G4429 bound to ASN G 442
31
DC4
SOFTWARE
ASN G:464A , NAG G:3551
Binding site for Poly-Saccharide residues NAG G4641A through NAG G4642A bound to ASN G 464A
32
DC5
SOFTWARE
ASN H:23 , LEU H:77
Binding site for Poly-Saccharide residues NAG H 231 through MAN H 238 bound to ASN H 23
33
DC6
SOFTWARE
ILE V:20 , SER V:65 , ARG V:66 , ASN V:72
Binding site for Poly-Saccharide residues NAG V 721 through MAN V 728 bound to ASN V 72
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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all CATH domains
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Pfam Domains
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