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4RFN
Asym. Unit
Info
Asym.Unit (534 KB)
Biol.Unit 1 (266 KB)
Biol.Unit 2 (265 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ADCC-POTENT RHESUS MACAQUE ANTIBODY JR4 IN COMPLEX WITH HIV-1 CLADE A/E GP120 AND M48
Authors
:
N. Gohain, W. D. Tolbert, M. Pazgier
Date
:
26 Sep 14 (Deposition) - 15 Jul 15 (Release) - 19 Aug 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.21
Chains
:
Asym. Unit : A,B,C,D,G,H,L,M
Biol. Unit 1: G,H,L,M (1x)
Biol. Unit 2: A,B,C,D (1x)
Keywords
:
Hiv-1 Gp120, Viral Protein, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Gohain, W. D. Tolbert, P. Acharya, L. Yu, T. Liu, P. Zhao, C. Orlandi, M. L. Visciano, R. Kamin-Lewis, M. M. Sajadi, L. Martin, J. E. Robinson P. D. Kwong, A. L. Devico, K. Ray, G. K. Lewis, M. Pazgier
Cocrystal Structures Of Antibody N60-I3 And Antibody Jr4 In Complex With Gp120 Define More Cluster A Epitopes Involved In Effective Antibody-Dependent Effector Function Against Hiv-1.
J. Virol. V. 89 8840 2015
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Hetero Components
(4, 24)
Info
All Hetero Components
1a: D-PROLINE (DPRa)
1b: D-PROLINE (DPRb)
2a: BETA-MERCAPTOPROPIONIC ACID (MPTa)
2b: BETA-MERCAPTOPROPIONIC ACID (MPTb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
4a: AMINO GROUP (NH2a)
4b: AMINO GROUP (NH2b)
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Select:
Label:
No.
Name
Count
Type
Full Name
1
DPR
2
Mod. Amino Acid
D-PROLINE
2
MPT
2
Mod. Amino Acid
BETA-MERCAPTOPROPIONIC ACID
3
NAG
18
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NH2
2
Mod. Amino Acid
AMINO GROUP
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Sites
(20, 20)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:474 , CYS M:19 , ALA M:20 , THR M:22 , PHE M:23
BINDING SITE FOR RESIDUE DPR M 21
02
AC2
SOFTWARE
GLY A:473 , CYS D:19 , ALA D:20 , THR D:22 , PHE D:23
BINDING SITE FOR RESIDUE DPR D 21
03
AC3
SOFTWARE
ASN G:234 , THR G:236 , SER G:274
BINDING SITE FOR RESIDUE NAG G 501
04
AC4
SOFTWARE
ASN G:229 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 502
05
AC5
SOFTWARE
PRO G:212 , LYS G:252 , ASN G:262 , PHE G:376 , ASN G:377 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447
BINDING SITE FOR RESIDUE NAG G 503
06
AC6
SOFTWARE
ASN G:276 , THR G:278
BINDING SITE FOR RESIDUE NAG G 504
07
AC7
SOFTWARE
GLU G:269 , ILE G:270 , ASN G:289 , LYS G:290 , GLN G:344
BINDING SITE FOR RESIDUE NAG G 505
08
AC8
SOFTWARE
GLU G:293 , ASN G:295 , THR G:297 , GLU G:332 , LYS G:442
BINDING SITE FOR RESIDUE NAG G 506
09
AC9
SOFTWARE
ASN G:334 , THR G:336 , LYS G:337 , THR G:413
BINDING SITE FOR RESIDUE NAG G 507
10
BC1
SOFTWARE
THR G:372 , ASN G:386 , THR G:388
BINDING SITE FOR RESIDUE NAG G 508
11
BC2
SOFTWARE
ASN G:392
BINDING SITE FOR RESIDUE NAG G 509
12
BC3
SOFTWARE
ASN A:234 , THR A:236 , SER A:274
BINDING SITE FOR RESIDUE NAG A 501
13
BC4
SOFTWARE
HIS A:85 , ASN A:229 , LYS A:231 , ASN A:241 , GLU A:267
BINDING SITE FOR RESIDUE NAG A 502
14
BC5
SOFTWARE
LYS A:252 , VAL A:254 , ASN A:262 , ARG A:379 , CYS A:445 , VAL A:446 , SER A:447
BINDING SITE FOR RESIDUE NAG A 503
15
BC6
SOFTWARE
ASN A:276 , THR A:278 , ASN A:279
BINDING SITE FOR RESIDUE NAG A 504
16
BC7
SOFTWARE
GLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLN A:344
BINDING SITE FOR RESIDUE NAG A 505
17
BC8
SOFTWARE
GLU A:293 , ASN A:295 , THR A:297 , LYS A:442
BINDING SITE FOR RESIDUE NAG A 506
18
BC9
SOFTWARE
ASN A:334 , THR A:336 , ASN A:411
BINDING SITE FOR RESIDUE NAG A 507
19
CC1
SOFTWARE
THR A:372 , ASN A:386 , THR A:388
BINDING SITE FOR RESIDUE NAG A 508
20
CC2
SOFTWARE
GLN A:389 , ASN A:392 , GLY A:409 , CYS A:410
BINDING SITE FOR RESIDUE NAG A 509
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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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Pfam Domains
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Asymmetric Unit 1
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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
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ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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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 (534 KB)
Header - Asym.Unit
Biol.Unit 1 (266 KB)
Header - Biol.Unit 1
Biol.Unit 2 (265 KB)
Header - Biol.Unit 2
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