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4ID5
Asym. Unit
Info
Asym.Unit (362 KB)
Biol.Unit 1 (353 KB)
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(1)
Title
:
HIV-1 REVERSE TRANSCRIPTASE WITH BOUND FRAGMENT AT THE RNASE H PRIMER GRIP SITE
Authors
:
J. D. Bauman, D. Patel, E. Arnold
Date
:
11 Dec 12 (Deposition) - 06 Feb 13 (Release) - 17 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rna-Directed Dna Polymerase, Dna Polymerase, Endonuclease, Hydrolase, Multifunctional Enzyme, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. D. Bauman, D. Patel, C. Dharia, M. W. Fromer, S. Ahmed, Y. Frenkel, R. S. Vijayan, J. T. Eck, W. C. Ho, K. Das, A. J. Shatkin, E. Arnold
Detecting Allosteric Sites Of Hiv-1 Reverse Transcriptase B X-Ray Crystallographic Fragment Screening.
J. Med. Chem. V. 56 2738 2013
[
close entry info
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Hetero Components
(4, 20)
Info
All Hetero Components
1a: 1-METHYL-5-PHENYL-1H-PYRAZOLE-4-CA... (1FFa)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
2e: DIMETHYL SULFOXIDE (DMSe)
2f: DIMETHYL SULFOXIDE (DMSf)
2g: DIMETHYL SULFOXIDE (DMSg)
2h: DIMETHYL SULFOXIDE (DMSh)
2i: DIMETHYL SULFOXIDE (DMSi)
2j: DIMETHYL SULFOXIDE (DMSj)
2k: DIMETHYL SULFOXIDE (DMSk)
2l: DIMETHYL SULFOXIDE (DMSl)
2m: DIMETHYL SULFOXIDE (DMSm)
2n: DIMETHYL SULFOXIDE (DMSn)
2o: DIMETHYL SULFOXIDE (DMSo)
2p: DIMETHYL SULFOXIDE (DMSp)
2q: DIMETHYL SULFOXIDE (DMSq)
3a: MAGNESIUM ION (MGa)
4a: 4-{[4-({4-[(E)-2-CYANOETHENYL]-2,6... (T27a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1FF
1
Ligand/Ion
1-METHYL-5-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACID
2
DMS
17
Ligand/Ion
DIMETHYL SULFOXIDE
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
T27
1
Ligand/Ion
4-{[4-({4-[(E)-2-CYANOETHENYL]-2,6-DIMETHYLPHENYL}AMINO)PYRIMIDIN-2-YL]AMINO}BENZONITRILE
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:100 , LYS A:101 , TYR A:181 , TYR A:188 , PHE A:227 , TRP A:229 , LEU A:234 , HIS A:235 , PRO A:236 , TYR A:318 , HOH A:1023 , GLU B:138 , HOH B:661
BINDING SITE FOR RESIDUE T27 A 601
02
AC2
SOFTWARE
LYS A:331 , GLN A:334 , LYS A:512
BINDING SITE FOR RESIDUE DMS A 602
03
AC3
SOFTWARE
TRP A:401 , LEU A:425 , TRP A:426 , TYR A:427 , GLN A:509 , ASP A:511
BINDING SITE FOR RESIDUE DMS A 603
04
AC4
SOFTWARE
TYR A:427 , GLN A:428 , LEU A:525 , LYS A:528 , GLU A:529
BINDING SITE FOR RESIDUE DMS A 604
05
AC5
SOFTWARE
ARG A:72 , LYS A:73 , TYR A:146 , GLN A:151 , HOH A:1094 , HOH A:1097 , HOH A:1153
BINDING SITE FOR RESIDUE DMS A 605
06
AC6
SOFTWARE
ARG A:448 , THR A:473 , ASN A:474 , GLN A:475
BINDING SITE FOR RESIDUE DMS A 606
07
AC7
SOFTWARE
THR A:403 , GLU A:404 , HOH A:958 , LYS B:331 , GLN B:332
BINDING SITE FOR RESIDUE DMS A 607
08
AC8
SOFTWARE
LYS A:323 , ASP A:324
BINDING SITE FOR RESIDUE DMS A 608
09
AC9
SOFTWARE
LYS A:476 , GLN A:480 , TYR A:483 , LEU A:517 , GLN A:520 , HOH A:864 , HOH A:984
BINDING SITE FOR RESIDUE 1FF A 609
10
BC1
SOFTWARE
ASP A:443 , ASP A:498 , ASP A:549 , HOH A:875 , HOH A:907 , HOH A:1151
BINDING SITE FOR RESIDUE MG A 610
11
BC2
SOFTWARE
THR B:27 , THR B:400 , TRP B:401 , GLU B:404
BINDING SITE FOR RESIDUE DMS B 501
12
BC3
SOFTWARE
GLN A:85 , TYR B:56 , LYS B:126 , HOH B:805
BINDING SITE FOR RESIDUE DMS B 502
13
BC4
SOFTWARE
ILE A:380 , VAL A:381 , PRO B:25 , LEU B:26 , PRO B:133 , SER B:134 , ILE B:135 , ASN B:136
BINDING SITE FOR RESIDUE DMS B 503
14
BC5
SOFTWARE
TRP B:337 , ARG B:356 , MET B:357 , GLN B:367
BINDING SITE FOR RESIDUE DMS B 504
15
BC6
SOFTWARE
LEU B:234 , HIS B:235 , TRP B:239 , HOH B:883
BINDING SITE FOR RESIDUE DMS B 505
16
BC7
SOFTWARE
TRP B:24 , GLU B:399 , TRP B:402 , HOH B:634
BINDING SITE FOR RESIDUE DMS B 506
17
BC8
SOFTWARE
ASN B:265 , GLN B:269 , TRP B:426
BINDING SITE FOR RESIDUE DMS B 507
18
BC9
SOFTWARE
PRO B:243 , ILE B:244 , VAL B:245 , LYS B:263 , TRP B:426 , TYR B:427 , GLN B:428
BINDING SITE FOR RESIDUE DMS B 508
19
CC1
SOFTWARE
TYR B:271 , ASN B:348 , HOH B:940
BINDING SITE FOR RESIDUE DMS B 509
20
CC2
SOFTWARE
LEU A:168 , HOH A:846 , HOH A:894 , PRO B:140
BINDING SITE FOR RESIDUE DMS B 510
[
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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
;
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Sorry, no Info available
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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
(2, 3)
Info
All SCOP Domains
1a: SCOP_d4id5a2 (A:430-554)
2a: SCOP_d4id5a1 (A:-1-429)
2b: SCOP_d4id5b_ (B:)
View:
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Classes
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Folds
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Superfamilies
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
automated matches
(127)
Protein domain
:
automated matches
(127)
Human immunodeficiency virus type 1 [TaxId: 11678]
(14)
1a
d4id5a2
A:430-554
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Reverse transcriptase
(217)
Protein domain
:
automated matches
(34)
Human immunodeficiency virus type 1 [TaxId: 11678]
(12)
2a
d4id5a1
A:-1-429
2b
d4id5b_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
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Example Commands
Example Command
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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).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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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).
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Asym.Unit (362 KB)
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Header - Biol.Unit 1
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