PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2B5J
Asym. Unit
Info
Asym.Unit (170 KB)
Biol.Unit 1 (164 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH JANSSEN-R165481
Authors
:
D. H. Himmel, K. Das, A. D. Clark Jr. , S. H. Hughes, A. Benjahad, S. Oumouch, J. Guillemont, S. Coupa, A. Poncelet, I. Csoka, C. Meyer, K. Andries, C. H. Mguyen, D. S. Grierson, E. Arnold
Date
:
28 Sep 05 (Deposition) - 06 Dec 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Aids, Hiv, Drug Design, Reverse Transcriptase, Rt, Protein- Inhibitor Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Himmel, K. Das, A. D. Clark Jr. , S. H. Hughes, A. Benjahad, S. Oumouch, J. Guillemont, S. Coupa, A. Poncelet, I. Csoka, C. Meyer, K. Andries, C. H. Nguyen, D. S. Grierson, E. Arnold
Crystal Structures For Hiv-1 Reverse Transcriptase In Complexes With Three Pyridinone Derivatives: A New Class Of Non-Nucleoside Inhibitors Effective Against A Broad Range Of Drug-Resistant Strains.
J. Med. Chem. V. 48 7582 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: (2E)-3-{3-[(5-ETHYL-3-IODO-6-METHY... (3ACa)
2a: MANGANESE (II) ION (MNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3AC
1
Ligand/Ion
(2E)-3-{3-[(5-ETHYL-3-IODO-6-METHYL-2-OXO-1,2-DIHYDROPYRIDIN-4-YL)OXY]PHENYL}ACRYLONITRILE
2
MN
1
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:443 , GLY A:444 , GLU A:478 , ASP A:498 , HOH A:1001
BINDING SITE FOR RESIDUE MN A 561
2
AC2
SOFTWARE
LEU A:100 , LYS A:101 , VAL A:106 , TYR A:188 , GLY A:190 , PHE A:227 , TRP A:229 , LEU A:234 , TYR A:318
BINDING SITE FOR RESIDUE 3AC A 562
[
close Site info
]
SAPs(SNPs)/Variants
(5, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_POL_HV1B1_003 (K172R, chain A/B, )
2: VAR_POL_HV1B1_004 (K451R, chain A, )
3: VAR_POL_HV1B1_005 (V458L, chain A, )
4: VAR_POL_HV1B1_006 (K512Q, chain A, )
5: VAR_POL_HV1B1_007 (E529Q, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_POL_HV1B1_003
*
K
771
R
POL_HV1B1
---
---
A/B
K
172
R
2
UniProt
VAR_POL_HV1B1_004
*
K
1050
R
POL_HV1B1
---
---
A
K
451
R
3
UniProt
VAR_POL_HV1B1_005
*
V
1057
L
POL_HV1B1
---
---
A
V
458
L
4
UniProt
VAR_POL_HV1B1_006
*
K
1111
Q
POL_HV1B1
---
---
A
K
512
Q
5
UniProt
VAR_POL_HV1B1_007
*
E
1128
Q
POL_HV1B1
---
---
A
E
529
Q
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: RT_POL (A:44-234,B:44-234)
2: RNASE_H (A:434-552)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RT_POL
PS50878
Reverse transcriptase (RT) catalytic domain profile.
POL_HV1B1
643-833
2
A:44-234
B:44-234
2
RNASE_H
PS50879
RNase H domain profile.
POL_HV1B1
1033-1156
1
A:434-552
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(2, 3)
Info
All SCOP Domains
1a: SCOP_d2b5ja2 (A:430-552)
2a: SCOP_d2b5ja1 (A:1-429)
2b: SCOP_d2b5jb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
Ribonuclease H
(190)
Protein domain
:
HIV RNase H (Domain of reverse transcriptase)
(110)
Human immunodeficiency virus type 1 [TaxId: 11676]
(101)
1a
d2b5ja2
A:430-552
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Reverse transcriptase
(217)
Protein domain
:
HIV-1 reverse transcriptase
(161)
Human immunodeficiency virus type 1 [TaxId: 11676]
(138)
2a
d2b5ja1
A:1-429
2b
d2b5jb_
B:
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_2b5jB02 (B:99-123,B:165-233)
1b: CATH_2b5jA02 (A:91-115,A:157-225)
1c: CATH_2b5jA03 (A:226-319)
1d: CATH_2b5jB03 (B:234-319)
1e: CATH_2b5jA04 (A:320-426)
1f: CATH_2b5jB04 (B:320-426)
2a: CATH_2b5jA05 (A:427-552)
3a: CATH_2b5jA01 (A:1-90,A:116-156)
3b: CATH_2b5jB01 (B:9-98,B:124-164)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.270, no name defined]
(278)
Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: bh10 isolate.
(1)
1a
2b5jB02
B:99-123,B:165-233
1b
2b5jA02
A:91-115,A:157-225
1c
2b5jA03
A:226-319
1d
2b5jB03
B:234-319
1e
2b5jA04
A:320-426
1f
2b5jB04
B:320-426
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: bh10 isolate.
(1)
2a
2b5jA05
A:427-552
Architecture
:
Roll
(3276)
Topology
:
HIV Type 1 Reverse Transcriptase; Chain A, domain 1
(164)
Homologous Superfamily
:
HIV Type 1 Reverse Transcriptase, subunit A, domain 1
(164)
Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: bh10 isolate.
(1)
3a
2b5jA01
A:1-90,A:116-156
3b
2b5jB01
B:9-98,B:124-164
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (170 KB)
Header - Asym.Unit
Biol.Unit 1 (164 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2B5J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
