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4RZ8
Asym. Unit
Info
Asym.Unit (496 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (124 KB)
Biol.Unit 3 (126 KB)
Biol.Unit 4 (126 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 GP120 CORE IN COMPLEX WITH NBD-11021, A SMALL MOLECULE CD4-ANTAGONIST
Authors
:
Y. D. Kwon, A. K. Debnath, P. D. Kwong
Date
:
18 Dec 14 (Deposition) - 09 Sep 15 (Release) - 23 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Hiv-1 Gp120, Nbd-11021, Small Molecule Cd4-Antagonist, Phe 43 Cavity, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Curreli, Y. D. Kwon, H. Zhang, D. Scacalossi, D. S. Belov, A. A. Tikhonov, I. A. Andreev, A. Altieri, A. V. Kurkin, P. D. Kwong, A. K. Debnath
Structure-Based Design Of A Small Molecule Cd4-Antagonist With Broad Spectrum Anti-Hiv-1 Activity.
J. Med. Chem. V. 58 6909 2015
[
close entry info
]
Hetero Components
(3, 48)
Info
All Hetero Components
1a: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMa)
1b: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMb)
1c: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMc)
1d: 5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDR... (3ZMd)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
3ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
3ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
3ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
3ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
3af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
3ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
3ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
3ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
3aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
3ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
3al: N-ACETYL-D-GLUCOSAMINE (NAGal)
3am: N-ACETYL-D-GLUCOSAMINE (NAGam)
3an: N-ACETYL-D-GLUCOSAMINE (NAGan)
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)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
3z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3ZM
4
Ligand/Ion
5-(4-CHLOROPHENYL)-N-{(S)-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL][(2R)-PIPERIDIN-2-YL]METHYL}-1H-PYRROLE-2-CARBOXAMIDE
2
EPE
4
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
NAG
40
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(48, 48)
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)
48: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:234 , THR A:236
BINDING SITE FOR RESIDUE NAG A 501
02
AC2
SOFTWARE
HIS A:85 , ASN A:229 , ASN A:241
BINDING SITE FOR RESIDUE NAG A 502
03
AC3
SOFTWARE
LEU A:261 , ASN A:262 , ARG A:379 , CYS A:445 , VAL A:446 , SER A:447 , NAG A:509 , HOH A:603 , HOH A:611 , HOH A:612 , HOH A:687
BINDING SITE FOR RESIDUE NAG A 503
04
AC4
SOFTWARE
ASN A:276 , ASN A:279
BINDING SITE FOR RESIDUE NAG A 504
05
AC5
SOFTWARE
GLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , LYS A:348 , LYS D:59 , HIS D:61
BINDING SITE FOR RESIDUE NAG A 505
06
AC6
SOFTWARE
ASN A:295 , TYR A:330 , HOH A:682
BINDING SITE FOR RESIDUE NAG A 506
07
AC7
SOFTWARE
ASN A:334 , THR A:413
BINDING SITE FOR RESIDUE NAG A 507
08
AC8
SOFTWARE
MET A:373 , ASN A:386 , THR A:388 , GLN B:203
BINDING SITE FOR RESIDUE NAG A 508
09
AC9
SOFTWARE
ASN A:262 , ASN A:448 , NAG A:503
BINDING SITE FOR RESIDUE NAG A 509
10
BC1
SOFTWARE
ASP A:368 , GLU A:370 , SER A:375 , PHE A:376 , ASN A:377 , PHE A:382 , ASN A:425 , MET A:426 , TRP A:427 , GLN A:428 , GLY A:429
BINDING SITE FOR RESIDUE 3ZM A 510
11
BC2
SOFTWARE
LEU A:52 , CYS A:54 , ALA A:73 , GLN A:103 , ASP A:107 , TYR A:217 , ARG B:327 , LYS B:421 , GLN B:422 , ILE B:423
BINDING SITE FOR RESIDUE EPE A 511
12
BC3
SOFTWARE
ASN B:234 , THR B:236 , HIS B:352
BINDING SITE FOR RESIDUE NAG B 501
13
BC4
SOFTWARE
ASN B:229 , ASN B:241
BINDING SITE FOR RESIDUE NAG B 502
14
BC5
SOFTWARE
LEU B:261 , ASN B:262 , ARG B:379 , CYS B:445 , VAL B:446 , SER B:447 , NAG B:509 , HOH B:603 , HOH B:606 , HOH B:610 , HOH B:616 , ASN C:354 , ASN C:355 , SER C:464
BINDING SITE FOR RESIDUE NAG B 503
15
BC6
SOFTWARE
ASN B:276 , ASN B:279
BINDING SITE FOR RESIDUE NAG B 504
16
BC7
SOFTWARE
GLU B:268 , ILE B:270 , ASN B:289
BINDING SITE FOR RESIDUE NAG B 505
17
BC8
SOFTWARE
ASN B:295 , TYR B:330 , VAL B:446 , HOH B:660 , HOH C:703 , HOH C:747
BINDING SITE FOR RESIDUE NAG B 506
18
BC9
SOFTWARE
ASN B:334 , LYS B:337 , THR B:413 , HOH B:712
BINDING SITE FOR RESIDUE NAG B 507
19
CC1
SOFTWARE
ASN B:386 , THR B:388
BINDING SITE FOR RESIDUE NAG B 508
20
CC2
SOFTWARE
ASN B:262 , ASN B:448 , NAG B:503 , HOH B:613 , HOH B:685 , HOH B:719 , LYS C:350 , ASN C:355
BINDING SITE FOR RESIDUE NAG B 509
21
CC3
SOFTWARE
VAL B:255 , ASP B:368 , GLU B:370 , SER B:375 , PHE B:376 , ASN B:377 , ASN B:425 , MET B:426 , TRP B:427 , GLN B:428 , GLY B:429
BINDING SITE FOR RESIDUE 3ZM B 510
22
CC4
SOFTWARE
ARG A:327 , LYS A:421 , GLN A:422 , ILE A:423 , LEU B:52 , CYS B:54 , HIS B:72 , ALA B:73 , GLN B:103 , ASP B:107
BINDING SITE FOR RESIDUE EPE B 511
23
CC5
SOFTWARE
ASN C:234 , THR C:236 , HIS C:352 , HOH C:791
BINDING SITE FOR RESIDUE NAG C 501
24
CC6
SOFTWARE
LYS C:231 , LYS C:240 , ASN C:241
BINDING SITE FOR RESIDUE NAG C 502
25
CC7
SOFTWARE
LYS C:252 , ASN C:262 , ARG C:379 , CYS C:445 , VAL C:446 , SER C:447 , HOH C:617 , HOH C:626 , HOH C:627
BINDING SITE FOR RESIDUE NAG C 503
26
CC8
SOFTWARE
HIS B:61 , ASN C:276 , THR C:278 , ASN C:279
BINDING SITE FOR RESIDUE NAG C 504
27
CC9
SOFTWARE
GLU C:268 , GLU C:269 , ILE C:270 , ASN C:289 , HOH C:642 , HOH C:682 , HOH C:737
BINDING SITE FOR RESIDUE NAG C 505
28
DC1
SOFTWARE
ASN C:295 , GLU C:332 , VAL C:446
BINDING SITE FOR RESIDUE NAG C 506
29
DC2
SOFTWARE
ASN C:334 , THR C:336 , LYS C:337 , HOH C:749
BINDING SITE FOR RESIDUE NAG C 507
30
DC3
SOFTWARE
LYS B:252 , ASN C:354 , ASN C:355 , HOH C:660 , HOH C:701
BINDING SITE FOR RESIDUE NAG C 508
31
DC4
SOFTWARE
ASN C:386 , THR C:388
BINDING SITE FOR RESIDUE NAG C 509
32
DC5
SOFTWARE
ASN C:392 , THR C:394 , CYS C:395
BINDING SITE FOR RESIDUE NAG C 510
33
DC6
SOFTWARE
SER C:291 , ASN C:448 , HOH C:667
BINDING SITE FOR RESIDUE NAG C 511
34
DC7
SOFTWARE
ASP C:368 , GLU C:370 , SER C:375 , PHE C:376 , ASN C:377 , PHE C:382 , ASN C:425 , MET C:426 , TRP C:427 , GLN C:428 , GLY C:429 , HOH C:677
BINDING SITE FOR RESIDUE 3ZM C 512
35
DC8
SOFTWARE
LEU C:52 , CYS C:54 , HIS C:72 , ALA C:73 , GLN C:103 , ASP C:107 , HOH C:684 , HOH C:700 , HOH C:752
BINDING SITE FOR RESIDUE EPE C 513
36
DC9
SOFTWARE
ASN D:234 , THR D:236 , HIS D:352
BINDING SITE FOR RESIDUE NAG D 501
37
EC1
SOFTWARE
ASP D:230 , LYS D:240 , ASN D:241 , HOH D:740
BINDING SITE FOR RESIDUE NAG D 502
38
EC2
SOFTWARE
LYS D:252 , ASN D:262 , CYS D:445 , VAL D:446 , SER D:447 , HOH D:607 , HOH D:609 , HOH D:610
BINDING SITE FOR RESIDUE NAG D 503
39
EC3
SOFTWARE
ASN D:276 , ASN D:279
BINDING SITE FOR RESIDUE NAG D 504
40
EC4
SOFTWARE
GLU D:268 , GLU D:269 , ILE D:270 , ASN D:289 , HOH D:613 , HOH D:751
BINDING SITE FOR RESIDUE NAG D 505
41
EC5
SOFTWARE
ASN D:295 , GLU D:332
BINDING SITE FOR RESIDUE NAG D 506
42
EC6
SOFTWARE
ASN D:334 , THR D:336 , LYS D:337 , HOH D:766 , HOH D:812
BINDING SITE FOR RESIDUE NAG D 507
43
EC7
SOFTWARE
ASN D:355 , HOH D:733
BINDING SITE FOR RESIDUE NAG D 508
44
EC8
SOFTWARE
ASN D:386 , THR D:388
BINDING SITE FOR RESIDUE NAG D 509
45
EC9
SOFTWARE
ASN D:392 , CYS D:395
BINDING SITE FOR RESIDUE NAG D 510
46
FC1
SOFTWARE
SER D:291 , ASN D:448 , HOH D:716
BINDING SITE FOR RESIDUE NAG D 511
47
FC2
SOFTWARE
ASP D:368 , GLU D:370 , SER D:375 , PHE D:376 , ASN D:377 , PHE D:382 , ASN D:425 , MET D:426 , TRP D:427 , GLN D:428 , GLY D:429 , GLY D:473 , HOH D:830 , HOH D:831
BINDING SITE FOR RESIDUE 3ZM D 512
48
FC3
SOFTWARE
LEU D:52 , HIS D:72 , ALA D:73 , GLN D:103 , ASP D:107 , HOH D:652 , HOH D:658 , HOH D:784
BINDING SITE FOR RESIDUE EPE D 513
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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]
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (496 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (124 KB)
Header - Biol.Unit 2
Biol.Unit 3 (126 KB)
Header - Biol.Unit 3
Biol.Unit 4 (126 KB)
Header - Biol.Unit 4
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