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Getting 'Biological Unit' information from database.
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3I6O
Asym. Unit
Info
Asym.Unit (88 KB)
Biol.Unit 1 (83 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF WILD TYPE HIV-1 PROTEASE WITH MACROCYCLIC INHIBITOR GRL-0216A
Authors
:
A. A. Chumanevich, Y. -F. Wang, A. Y. Kovalevsky, I. T. Weber
Date
:
07 Jul 09 (Deposition) - 29 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.17
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hiv-1, Wild Type Protease, Protease Inhibitor, Macrocyclic Ligand, Aids, Aspartyl Protease, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. K. Ghosh, S. Kulkarni, D. D. Anderson, L. Hong, A. Baldridge, Y. F. Wang, A. A. Chumanevich, A. Y. Kovalevsky, Y. Tojo, M. Amano, Y. Koh, J. Tang, I. T. Weber, H. Mitsuya
Design, Synthesis, Protein-Ligand X-Ray Structure, And Biological Evaluation Of A Series Of Novel Macrocyclic Huma Immunodeficiency Virus-1 Protease Inhibitors To Combat Drug Resistance.
J. Med. Chem. V. 52 7689 2009
[
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Hetero Components
(4, 24)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]F... (GR6a)
3a: IODIDE ION (IODa)
3b: IODIDE ION (IODb)
3c: IODIDE ION (IODc)
3d: IODIDE ION (IODd)
3e: IODIDE ION (IODe)
3f: IODIDE ION (IODf)
3g: IODIDE ION (IODg)
3h: IODIDE ION (IODh)
3i: IODIDE ION (IODi)
3j: IODIDE ION (IODj)
3k: IODIDE ION (IODk)
3l: IODIDE ION (IODl)
3m: IODIDE ION (IODm)
3n: IODIDE ION (IODn)
3o: IODIDE ION (IODo)
3p: IODIDE ION (IODp)
3q: IODIDE ION (IODq)
3r: IODIDE ION (IODr)
3s: IODIDE ION (IODs)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
GR6
1
Ligand/Ion
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL {(1S,2R)-1-BENZYL-2-HYDROXY-3-[(7E)-13-METHOXY-1,1-DIOXIDO-3,4,5,6,9,10-HEXAHYDRO-2H-11,1,2-BENZOXATHIAZACYCLOTRIDECIN-2-YL]PROPYL}CARBAMATE
3
IOD
19
Ligand/Ion
IODIDE ION
4
NA
2
Ligand/Ion
SODIUM ION
[
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]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:60 , HOH A:1023 , HOH A:1055 , HOH A:1076 , HOH A:1094 , HOH A:1107
BINDING SITE FOR RESIDUE NA A 201
02
AC2
SOFTWARE
THR A:74
BINDING SITE FOR RESIDUE IOD A 211
03
AC3
SOFTWARE
GLY A:48 , HOH A:1232
BINDING SITE FOR RESIDUE IOD A 216
04
AC4
SOFTWARE
THR A:12 , GLY A:68
BINDING SITE FOR RESIDUE IOD A 217
05
AC5
SOFTWARE
THR A:12
BINDING SITE FOR RESIDUE IOD A 220
06
AC6
SOFTWARE
GLN A:61 , IOD A:225
BINDING SITE FOR RESIDUE IOD A 224
07
AC7
SOFTWARE
IOD A:224
BINDING SITE FOR RESIDUE IOD A 225
08
AC8
SOFTWARE
LYS A:55 , HOH A:1195
BINDING SITE FOR RESIDUE IOD A 228
09
AC9
SOFTWARE
LYS A:14 , GLY A:16 , GLY A:17 , ILE A:63 , ILE A:64 , GLU A:65
BINDING SITE FOR RESIDUE GOL A 303
10
BC1
SOFTWARE
ASP B:160 , HOH B:1034 , HOH B:1048 , HOH B:1068 , HOH B:1069 , HOH B:1098
BINDING SITE FOR RESIDUE NA B 202
11
BC2
SOFTWARE
THR B:112
BINDING SITE FOR RESIDUE IOD B 212
12
BC3
SOFTWARE
HOH B:1124
BINDING SITE FOR RESIDUE IOD B 213
13
BC4
SOFTWARE
IOD B:215
BINDING SITE FOR RESIDUE IOD B 214
14
BC5
SOFTWARE
PRO B:144 , LYS B:155 , IOD B:214
BINDING SITE FOR RESIDUE IOD B 215
15
BC6
SOFTWARE
GLY B:148
BINDING SITE FOR RESIDUE IOD B 218
16
BC7
SOFTWARE
ILE B:163 , HOH B:1074
BINDING SITE FOR RESIDUE IOD B 219
17
BC8
SOFTWARE
HOH A:1231 , GLY B:140 , HOH B:1236
BINDING SITE FOR RESIDUE IOD B 221
18
BC9
SOFTWARE
ARG B:108
BINDING SITE FOR RESIDUE IOD B 222
19
CC1
SOFTWARE
HOH A:1237 , GLU B:165
BINDING SITE FOR RESIDUE IOD B 223
20
CC2
SOFTWARE
LYS A:55 , LYS B:170 , IOD B:227
BINDING SITE FOR RESIDUE IOD B 226
21
CC3
SOFTWARE
LYS A:55 , IOD B:226
BINDING SITE FOR RESIDUE IOD B 227
22
CC4
SOFTWARE
ARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , GLY A:48 , GLY A:49 , ILE A:50 , PRO A:81 , VAL A:82 , ILE A:84 , HOH A:1232 , ARG B:108 , ASP B:125 , GLY B:127 , ALA B:128 , ASP B:129 , ASP B:130 , GLY B:148 , GLY B:149 , ILE B:150 , PRO B:181 , VAL B:182 , ILE B:184 , HOH B:1001 , HOH B:1253
BINDING SITE FOR RESIDUE GR6 B 301
23
CC5
SOFTWARE
LEU A:5 , TRP A:6 , ASP B:129 , ARG B:187 , ASN B:188 , THR B:191
BINDING SITE FOR RESIDUE GOL B 302
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ASP_PROT_RETROV (A:20-89,B:120-189)
2: ASP_PROTEASE (A:22-32,B:122-132)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ASP_PROT_RETROV
PS50175
Aspartyl protease, retroviral-type family profile.
POL_HV1BR
520-589
2
A:20-89
B:120-189
2
ASP_PROTEASE
PS00141
Eukaryotic and viral aspartyl proteases active site.
POL_HV1BR
522-533
2
A:22-32
B:122-132
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3i6oa_ (A:)
1b: SCOP_d3i6ob_ (B:)
View:
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Acid proteases
(1120)
Superfamily
:
Acid proteases
(1120)
Family
:
Retroviral protease (retropepsin)
(591)
Protein domain
:
Human immunodeficiency virus type 1 protease
(514)
Human immunodeficiency virus type 1 (bru isolate) [TaxId: 11686]
(20)
1a
d3i6oa_
A:
1b
d3i6ob_
B:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3i6oA00 (A:1-99)
1b: CATH_3i6oB00 (B:101-199)
View:
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Classes
(
)
(
)
Architectures
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(
)
Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Cathepsin D, subunit A; domain 1
(745)
Homologous Superfamily
:
Acid Proteases
(745)
Hiv-1 (Human immunodeficiency virus type 1 (bru isolate))
(6)
1a
3i6oA00
A:1-99
1b
3i6oB00
B:101-199
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
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Asymmetric Unit 1
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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)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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