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5F9W
Biol. Unit 2
Info
Asym.Unit (545 KB)
Biol.Unit 1 (268 KB)
Biol.Unit 2 (268 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING VH1-46 GERMLINE-DERIVED CD4-BINDING SITE-DIRECTED ANTIBODY CH235 IN COMPLEX WITH HIV-1 CLADE A/E 93TH057 GP120
Authors
:
L. Chen, T. Zhou, P. D. Kwong
Date
:
10 Dec 15 (Deposition) - 09 Mar 16 (Release) - 20 Apr 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.89
Chains
:
Asym. Unit : A,B,C,G,H,L
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: G,H,L (1x)
Keywords
:
Hiv-1, Vh1-46 Germline, Neutralizing Antibody, Ch235, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Bonsignori, T. Zhou, Z. Sheng, L. Chen, F. Gao, M. G. Joyce, G. Ozorowski, G. Y. Chuang, C. A. Schramm, K. Wiehe, S. M. Alam, T. Bradley, M. A. Gladden, K. K. Hwang, S. Iyengar, A. Kumar, X. Lu, K. Luo, M. C. Mangiapani, R. J. Parks, H. Song, P. Acharya, R. T. Bailer, A. Cao, A. Druz, I. S. Georgiev, Y. D. Kwon, M. K. Louder, B. Zhang, A. Zheng, B. J. Hill, R. Kong, C. Soto, J. C. Mullikin, D. C. Douek, D. C. Montefiori, M. A. Moody, G. M. Shaw, B. H. Hahn, G. Kelsoe, P. T. Hraber, B. T. Korber, S. D. Boyd, A. Z. Fire, T. B. Kepler, L. Shapiro, A. B. Ward, J. R. Mascola, H. X. Liao, P. D. Kwong, B. F. Hayne
Maturation Pathway From Germline To Broad Hiv-1 Neutralizer Of A Cd4-Mimic Antibody.
Cell V. 165 449 2016
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Hetero Components
(2, 14)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
1s: N-ACETYL-D-GLUCOSAMINE (NAGs)
1t: N-ACETYL-D-GLUCOSAMINE (NAGt)
1u: N-ACETYL-D-GLUCOSAMINE (NAGu)
1v: N-ACETYL-D-GLUCOSAMINE (NAGv)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
1y: N-ACETYL-D-GLUCOSAMINE (NAGy)
1z: N-ACETYL-D-GLUCOSAMINE (NAGz)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
PO4
1
Ligand/Ion
PHOSPHATE ION
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Sites
(17, 17)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC9 (SOFTWARE)
04: AD8 (SOFTWARE)
05: AD9 (SOFTWARE)
06: AE1 (SOFTWARE)
07: AE2 (SOFTWARE)
08: AE3 (SOFTWARE)
09: AE4 (SOFTWARE)
10: AE5 (SOFTWARE)
11: AE6 (SOFTWARE)
12: AE7 (SOFTWARE)
13: AE8 (SOFTWARE)
14: AE9 (SOFTWARE)
15: AF1 (SOFTWARE)
16: AF2 (SOFTWARE)
17: AF3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
THR H:28 , ASN H:31 , TYR H:32
binding site for residue PO4 H 301
02
AC3
SOFTWARE
GLU A:87 , ASN A:88 , ASP G:57
binding site for Mono-Saccharide NAG A 501 bound to ASN A 88
03
AC9
SOFTWARE
ASN A:295 , THR A:297 , TYR A:330 , GLU A:332 , LYS A:442 , SER L:182 , ASP L:185
binding site for Mono-Saccharide NAG A 507 bound to ASN A 295
04
AD8
SOFTWARE
ASN G:234 , THR G:236 , SER G:274 , ASN G:276
binding site for Mono-Saccharide NAG G 501 bound to ASN G 234
05
AD9
SOFTWARE
HIS G:85 , ASN G:229 , LYS G:231 , ASN G:241
binding site for Mono-Saccharide NAG G 502 bound to ASN G 241
06
AE1
SOFTWARE
LYS G:252 , ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , NAG G:512
binding site for Mono-Saccharide NAG G 503 bound to ASN G 262
07
AE2
SOFTWARE
ASN G:276 , HIS G:352 , PHE G:353 , HOH G:605 , ARG L:30
binding site for Mono-Saccharide NAG G 504 bound to ASN G 276
08
AE3
SOFTWARE
GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289
binding site for Mono-Saccharide NAG G 505 bound to ASN G 289
09
AE4
SOFTWARE
ASP C:185 , ASN G:295 , THR G:297 , TYR G:330 , GLU G:332 , LYS G:442
binding site for Mono-Saccharide NAG G 506 bound to ASN G 295
10
AE5
SOFTWARE
ASN G:334 , LYS G:337
binding site for Mono-Saccharide NAG G 507 bound to ASN G 334
11
AE6
SOFTWARE
ASN G:355
binding site for Mono-Saccharide NAG G 508 bound to ASN G 355
12
AE7
SOFTWARE
MET G:373 , ASN G:386 , THR G:388
binding site for Mono-Saccharide NAG G 509 bound to ASN G 386
13
AE8
SOFTWARE
GLN G:389 , ASN G:392 , THR G:394 , CYS G:410
binding site for Mono-Saccharide NAG G 510 bound to ASN G 392
14
AE9
SOFTWARE
LYS G:408 , GLY G:409 , ASN G:411
binding site for Mono-Saccharide NAG G 511 bound to ASN G 411
15
AF1
SOFTWARE
ASN G:262 , ASN G:448 , NAG G:503
binding site for Mono-Saccharide NAG G 512 bound to ASN G 448
16
AF2
SOFTWARE
ASN G:461 , THR G:463
binding site for Mono-Saccharide NAG G 513 bound to ASN G 461
17
AF3
SOFTWARE
GLU A:64 , HIS A:66 , SER A:209 , ASP A:211 , ARG A:327 , ASN A:377 , ARG A:379 , GLY A:380 , LYS A:419 , LYS H:209 , VAL H:211 , GLU H:212
binding site for Di-peptide PO4 A 515 and ARG H 210
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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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
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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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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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
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Show PDB file:
Asym.Unit (545 KB)
Header - Asym.Unit
Biol.Unit 1 (268 KB)
Header - Biol.Unit 1
Biol.Unit 2 (268 KB)
Header - Biol.Unit 2
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