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1QSY
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
DDATP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS
Authors
:
Y. Li, V. Mitaxov, G. Waksman
Date
:
24 Jun 99 (Deposition) - 16 Aug 99 (Release) - 23 Jun 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Protein-Dna Complex, Closed, Ddatp, Polymerase/Dna, Transferase-Dna Complex
(Keyword Search:
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Reference
:
Y. Li, V. Mitaxov, G. Waksman
Structure-Based Design Of Taq Dna Polymerases With Improved Properties Of Dideoxynucleotide Incorporation.
Proc. Natl. Acad. Sci. Usa V. 96 9491 1999
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: 2',3'-DIDEOXYADENOSINE-5'-MONOPHOS... (2DAa)
2a: 2',3'-DIDEOXYADENOSINE TRIPHOSPHAT... (DDSa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
2DA
1
Mod. Nucleotide
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2
DDS
1
Ligand/Ion
2',3'-DIDEOXYADENOSINE TRIPHOSPHATE
3
MG
2
Ligand/Ion
MAGNESIUM ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
DDS A:113 , ASP A:610 , TYR A:611 , ASP A:785 , MG A:1002
BINDING SITE FOR RESIDUE MG A 1001
2
AC2
SOFTWARE
DDS A:113 , ASP A:610 , ASP A:785 , MG A:1001 , HOH A:3139 , 2DA B:112 , HOH B:3019
BINDING SITE FOR RESIDUE MG A 1002
3
AC3
SOFTWARE
ARG A:573 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , LYS A:663 , PHE A:667 , ASP A:785 , MG A:1001 , MG A:1002 , HOH A:3049 , 2DA B:112 , HOH B:3019 , DT C:204 , DT C:205
BINDING SITE FOR RESIDUE DDS A 113
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_A (A:659-678)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPO1_THEAQ
659-678
1
A:659-678
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Exons
(0, 0)
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1qsya1 (A:293-422)
2a: SCOP_d1qsya2 (A:423-831)
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Protein Domains
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(
)
Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of prokaryotic DNA polymerase
(81)
Thermus aquaticus [TaxId: 271]
(24)
1a
d1qsya1
A:293-422
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
DNA polymerase I (Klenow fragment)
(82)
Thermus aquaticus [TaxId: 271]
(24)
2a
d1qsya2
A:423-831
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_1qsyA03 (A:564-613,A:758-831)
2a: CATH_1qsyA01 (A:293-446)
3a: CATH_1qsyA04 (A:614-757)
4a: CATH_1qsyA02 (A:447-563)
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Homologous Superfamilies
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.370, no name defined]
(99)
[unclassified]
(84)
1a
1qsyA03
A:564-613,A:758-831
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
2a
1qsyA01
A:293-446
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
3a
1qsyA04
A:614-757
Architecture
:
Up-down Bundle
(3216)
Topology
:
Taq DNA Polymerase; Chain T, domain 4
(88)
Homologous Superfamily
:
Taq DNA Polymerase; Chain T, domain 4
(88)
[unclassified]
(77)
4a
1qsyA02
A:447-563
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_DNA_pol_A_1qsyA01 (A:451-830)
2a: PFAM_Taq_exonuc_1qsyA02 (A:293-420)
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Clans
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Families
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Organisms
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)
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)
Clan
:
no clan defined [family: DNA_pol_A]
(69)
Family
:
DNA_pol_A
(69)
Thermus aquaticus
(17)
1a
DNA_pol_A-1qsyA01
A:451-830
Clan
:
no clan defined [family: Taq-exonuc]
(17)
Family
:
Taq-exonuc
(17)
Thermus aquaticus
(17)
2a
Taq-exonuc-1qsyA02
A:293-420
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Asymmetric Unit 1
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