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3EZ5
Asym. Unit
Info
Asym.Unit (224 KB)
Biol.Unit 1 (110 KB)
Biol.Unit 2 (112 KB)
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(1)
Title
:
COCRYSTAL STRUCTURE OF BACILLUS FRAGMENT DNA POLYMERASE I WITH DUPLEX DNA , DCTP, AND ZINC (CLOSED FORM).
Authors
:
J. J. Warren, E. Y. Wu, A. A. Golosov, M. Karplus, L. S. Beese
Date
:
22 Oct 08 (Deposition) - 10 Nov 09 (Release) - 02 Mar 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Protein-Dna Complex, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Golosov, J. J. Warren, L. S. Beese, M. Karplus
The Mechanism Of The Translocation Step In Dna Replication By Dna Polymerase I: A Computer Simulation Analysis.
Structure V. 18 83 2010
[
close entry info
]
Hetero Components
(4, 12)
Info
All Hetero Components
1a: 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSP... (DADa)
1b: 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSP... (DADb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
3a: SUCROSE (SUCa)
3b: SUCROSE (SUCb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DAD
2
Ligand/Ion
2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE
2
SO4
3
Ligand/Ion
SULFATE ION
3
SUC
2
Ligand/Ion
SUCROSE
4
ZN
5
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ZN A:4 , ZN A:5 , HOH A:127 , ARG A:615 , ASP A:653 , TYR A:654 , SER A:655 , GLN A:656 , ILE A:657 , GLU A:658 , HIS A:682 , ARG A:702 , LYS A:706 , ALA A:707 , TYR A:710 , ASP A:830 , DG B:29 , DT C:3 , DC C:4
BINDING SITE FOR RESIDUE DAD A 201
02
AC2
SOFTWARE
DAD A:201 , ASP A:653 , TYR A:654 , ASP A:830
BINDING SITE FOR RESIDUE ZN A 4
03
AC3
SOFTWARE
DAD A:201 , ASP A:653 , ASP A:830 , GLU A:831
BINDING SITE FOR RESIDUE ZN A 5
04
AC4
SOFTWARE
GLU A:325 , TYR A:327 , ASP A:372 , ARG A:375 , LEU A:395 , ASP A:408 , ILE A:605 , ASN A:607 , HOH A:897 , HOH A:913 , HOH A:919 , HOH A:924 , HOH A:941
BINDING SITE FOR RESIDUE SUC A 877
05
AC5
SOFTWARE
ARG A:306 , THR A:308 , GLU A:309
BINDING SITE FOR RESIDUE SO4 A 1
06
AC6
SOFTWARE
ARG A:779 , ASN A:780 , ARG D:423 , PRO D:424
BINDING SITE FOR RESIDUE SO4 A 2
07
AC7
SOFTWARE
ZN D:1 , ZN D:2 , HOH D:74 , HOH D:207 , ARG D:615 , ASP D:653 , TYR D:654 , SER D:655 , GLN D:656 , ILE D:657 , GLU D:658 , HIS D:682 , ARG D:702 , LYS D:706 , TYR D:710 , ASP D:830 , HOH D:1027 , DG E:29 , DT F:3 , DC F:4
BINDING SITE FOR RESIDUE DAD D 202
08
AC8
SOFTWARE
DAD D:202 , ASP D:653 , TYR D:654 , ASP D:830
BINDING SITE FOR RESIDUE ZN D 1
09
AC9
SOFTWARE
DAD D:202 , ASP D:653 , ASP D:830 , HOH D:968 , HOH D:1027
BINDING SITE FOR RESIDUE ZN D 2
10
BC1
SOFTWARE
ASP D:865 , HIS D:867
BINDING SITE FOR RESIDUE ZN D 3
11
BC2
SOFTWARE
GLU D:325 , TYR D:327 , ASP D:372 , ARG D:375 , ASP D:408 , ILE D:605 , ASN D:607 , HOH D:923 , HOH D:926 , HOH D:945 , HOH D:956 , HOH D:1015 , HOH D:1016
BINDING SITE FOR RESIDUE SUC D 877
12
BC3
SOFTWARE
HOH D:96 , MET D:299 , ALA D:300 , ARG D:343 , ARG D:677
BINDING SITE FOR RESIDUE SO4 D 878
[
close Site info
]
SAPs(SNPs)/Variants
(48, 96)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_DPO1_GEOSE_001 (K298K, chain A/D, )
02: VAR_DPO1_GEOSE_002 (A300A, chain A/D, )
03: VAR_DPO1_GEOSE_003 (R306R, chain A/D, )
04: VAR_DPO1_GEOSE_004 (E309E, chain A/D, )
05: VAR_DPO1_GEOSE_005 (V320L, chain A/D, )
06: VAR_DPO1_GEOSE_006 (D329D, chain A/D, )
07: VAR_DPO1_GEOSE_007 (H341H, chain A/D, )
08: VAR_DPO1_GEOSE_008 (Q356Q, chain A/D, )
09: VAR_DPO1_GEOSE_009 (V358V, chain A/D, )
10: VAR_DPO1_GEOSE_010 (S369S, chain A/D, )
11: VAR_DPO1_GEOSE_011 (C388C, chain A/D, )
12: VAR_DPO1_GEOSE_012 (S391S, chain A/D, )
13: VAR_DPO1_GEOSE_013 (A411R, chain A/D, )
14: VAR_DPO1_GEOSE_014 (A413A, chain A/D, )
15: VAR_DPO1_GEOSE_015 (K417K, chain A/D, )
16: VAR_DPO1_GEOSE_016 (P424P, chain A/D, )
17: VAR_DPO1_GEOSE_017 (A436A, chain A/D, )
18: VAR_DPO1_GEOSE_018 (V442V, chain A/D, )
19: VAR_DPO1_GEOSE_019 (E456E, chain A/D, )
20: VAR_DPO1_GEOSE_020 (R459R, chain A/D, )
21: VAR_DPO1_GEOSE_021 (V475V, chain A/D, )
22: VAR_DPO1_GEOSE_022 (E487E, chain A/D, )
23: VAR_DPO1_GEOSE_023 (A491A, chain A/D, )
24: VAR_DPO1_GEOSE_024 (K505K, chain A/D, )
25: VAR_DPO1_GEOSE_025 (A508R, chain A/D, )
26: VAR_DPO1_GEOSE_026 (Q510K, chain A/D, )
27: VAR_DPO1_GEOSE_027 (Q516Q, chain A/D, )
28: VAR_DPO1_GEOSE_028 (E540E, chain A/D, )
29: VAR_DPO1_GEOSE_029 (Y567Y, chain A/D, )
30: VAR_DPO1_GEOSE_030 (N573N, chain A/D, )
31: VAR_DPO1_GEOSE_031 (R596R, chain A/D, )
32: VAR_DPO1_GEOSE_032 (A598D, chain A/D, )
33: VAR_DPO1_GEOSE_033 (K600K, chain A/D, )
34: VAR_DPO1_GEOSE_034 (I605I, chain A/D, )
35: VAR_DPO1_GEOSE_035 (T619T, chain A/D, )
36: VAR_DPO1_GEOSE_036 (S645S, chain A/D, )
37: VAR_DPO1_GEOSE_037 (M672M, chain A/D, )
38: VAR_DPO1_GEOSE_038 (D678D, chain A/D, )
39: VAR_DPO1_GEOSE_039 (Q691Q, chain A/D, )
40: VAR_DPO1_GEOSE_040 (P699P, chain A/D, )
41: VAR_DPO1_GEOSE_041 (S728S, chain A/D, )
42: VAR_DPO1_GEOSE_042 (E741E, chain A/D, )
43: VAR_DPO1_GEOSE_043 (R748R, chain A/D, )
44: VAR_DPO1_GEOSE_044 (E751E, chain A/D, )
45: VAR_DPO1_GEOSE_045 (M790M, chain A/D, )
46: VAR_DPO1_GEOSE_046 (K816K, chain A/D, )
47: VAR_DPO1_GEOSE_047 (M841M, chain A/D, )
48: VAR_DPO1_GEOSE_048 (S870S, chain A/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_DPO1_GEOSE_001
*
G
298
K
DPO1_GEOSE
---
---
A/D
K
298
K
02
UniProt
VAR_DPO1_GEOSE_002
*
D
300
A
DPO1_GEOSE
---
---
A/D
A
300
A
03
UniProt
VAR_DPO1_GEOSE_003
*
S
306
R
DPO1_GEOSE
---
---
A/D
R
306
R
04
UniProt
VAR_DPO1_GEOSE_004
*
D
309
E
DPO1_GEOSE
---
---
A/D
E
309
E
05
UniProt
VAR_DPO1_GEOSE_005
*
V
320
L
DPO1_GEOSE
---
---
A/D
V
320
L
06
UniProt
VAR_DPO1_GEOSE_006
*
H
329
D
DPO1_GEOSE
---
---
A/D
D
329
D
07
UniProt
VAR_DPO1_GEOSE_007
*
R
341
H
DPO1_GEOSE
---
---
A/D
H
341
H
08
UniProt
VAR_DPO1_GEOSE_008
*
K
356
Q
DPO1_GEOSE
---
---
A/D
Q
356
Q
09
UniProt
VAR_DPO1_GEOSE_009
*
L
358
V
DPO1_GEOSE
---
---
A/D
V
358
V
10
UniProt
VAR_DPO1_GEOSE_010
*
T
369
S
DPO1_GEOSE
---
---
A/D
S
369
S
11
UniProt
VAR_DPO1_GEOSE_011
*
R
388
C
DPO1_GEOSE
---
---
A/D
C
388
C
12
UniProt
VAR_DPO1_GEOSE_012
*
V
391
S
DPO1_GEOSE
---
---
A/D
S
391
S
13
UniProt
VAR_DPO1_GEOSE_013
*
A
411
R
DPO1_GEOSE
---
---
A/D
A
411
R
14
UniProt
VAR_DPO1_GEOSE_014
*
V
413
A
DPO1_GEOSE
---
---
A/D
A
413
A
15
UniProt
VAR_DPO1_GEOSE_015
*
H
417
K
DPO1_GEOSE
---
---
A/D
K
417
K
16
UniProt
VAR_DPO1_GEOSE_016
*
S
424
P
DPO1_GEOSE
---
---
A/D
P
424
P
17
UniProt
VAR_DPO1_GEOSE_017
*
T
436
A
DPO1_GEOSE
---
---
A/D
A
436
A
18
UniProt
VAR_DPO1_GEOSE_018
*
T
442
V
DPO1_GEOSE
---
---
A/D
V
442
V
19
UniProt
VAR_DPO1_GEOSE_019
*
A
456
E
DPO1_GEOSE
---
---
A/D
E
456
E
20
UniProt
VAR_DPO1_GEOSE_020
*
E
459
R
DPO1_GEOSE
---
---
A/D
R
459
R
21
UniProt
VAR_DPO1_GEOSE_021
*
T
475
V
DPO1_GEOSE
---
---
A/D
V
475
V
22
UniProt
VAR_DPO1_GEOSE_022
*
N
487
E
DPO1_GEOSE
---
---
A/D
E
487
E
23
UniProt
VAR_DPO1_GEOSE_023
*
T
491
A
DPO1_GEOSE
---
---
A/D
A
491
A
24
UniProt
VAR_DPO1_GEOSE_024
*
A
505
K
DPO1_GEOSE
---
---
A/D
K
505
K
25
UniProt
VAR_DPO1_GEOSE_025
*
T
508
R
DPO1_GEOSE
---
---
A/D
A
508
R
26
UniProt
VAR_DPO1_GEOSE_026
*
Q
510
K
DPO1_GEOSE
---
---
A/D
Q
510
K
27
UniProt
VAR_DPO1_GEOSE_027
*
R
516
Q
DPO1_GEOSE
---
---
A/D
Q
516
Q
28
UniProt
VAR_DPO1_GEOSE_028
*
D
540
E
DPO1_GEOSE
---
---
A/D
E
540
E
29
UniProt
VAR_DPO1_GEOSE_029
*
H
567
Y
DPO1_GEOSE
---
---
A/D
Y
567
Y
30
UniProt
VAR_DPO1_GEOSE_030
*
H
573
N
DPO1_GEOSE
---
---
A/D
N
573
N
31
UniProt
VAR_DPO1_GEOSE_031
*
H
596
R
DPO1_GEOSE
---
---
A/D
R
596
R
32
UniProt
VAR_DPO1_GEOSE_032
*
V
598
D
DPO1_GEOSE
---
---
A/D
A
598
D
33
UniProt
VAR_DPO1_GEOSE_033
*
G
600
K
DPO1_GEOSE
---
---
A/D
K
600
K
34
UniProt
VAR_DPO1_GEOSE_034
*
M
605
I
DPO1_GEOSE
---
---
A/D
I
605
I
35
UniProt
VAR_DPO1_GEOSE_035
*
V
619
T
DPO1_GEOSE
---
---
A/D
T
619
T
36
UniProt
VAR_DPO1_GEOSE_036
*
P
645
S
DPO1_GEOSE
---
---
A/D
S
645
S
37
UniProt
VAR_DPO1_GEOSE_037
*
I
672
M
DPO1_GEOSE
---
---
A/D
M
672
M
38
UniProt
VAR_DPO1_GEOSE_038
*
G
678
D
DPO1_GEOSE
---
---
A/D
D
678
D
39
UniProt
VAR_DPO1_GEOSE_039
*
H
691
Q
DPO1_GEOSE
---
---
A/D
Q
691
Q
40
UniProt
VAR_DPO1_GEOSE_040
*
A
699
P
DPO1_GEOSE
---
---
A/D
P
699
P
41
UniProt
VAR_DPO1_GEOSE_041
*
T
728
S
DPO1_GEOSE
---
---
A/D
S
728
S
42
UniProt
VAR_DPO1_GEOSE_042
*
A
741
E
DPO1_GEOSE
---
---
A/D
E
741
E
43
UniProt
VAR_DPO1_GEOSE_043
*
Q
748
R
DPO1_GEOSE
---
---
A/D
R
748
R
44
UniProt
VAR_DPO1_GEOSE_044
*
D
751
E
DPO1_GEOSE
---
---
A/D
E
751
E
45
UniProt
VAR_DPO1_GEOSE_045
*
T
790
M
DPO1_GEOSE
---
---
A/D
M
790
M
46
UniProt
VAR_DPO1_GEOSE_046
*
R
816
K
DPO1_GEOSE
---
---
A/D
K
816
K
47
UniProt
VAR_DPO1_GEOSE_047
*
I
841
M
DPO1_GEOSE
---
---
A/D
M
841
M
48
UniProt
VAR_DPO1_GEOSE_048
*
P
870
S
DPO1_GEOSE
---
---
A/D
S
870
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_A (A:702-721,D:702-721)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_A
PS00447
DNA polymerase family A signature.
DPO1_GEOSE
702-721
2
A:702-721
D:702-721
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d3ez5a1 (A:297-468)
1b: SCOP_d3ez5d1 (D:298-468)
2a: SCOP_d3ez5a2 (A:469-876)
2b: SCOP_d3ez5d2 (D:469-876)
View:
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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
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of prokaryotic DNA polymerase
(81)
Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]
(43)
1a
d3ez5a1
A:297-468
1b
d3ez5d1
D:298-468
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)
Bacillus stearothermophilus, newly identified strain as yet unnamed [TaxId: 1422]
(44)
2a
d3ez5a2
A:469-876
2b
d3ez5d2
D:469-876
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_3ez5A03 (A:606-656,A:801-875)
1b: CATH_3ez5D03 (D:606-656,D:801-875)
2a: CATH_3ez5D01 (D:298-490)
2b: CATH_3ez5A01 (A:297-490)
3a: CATH_3ez5A04 (A:657-800)
3b: CATH_3ez5D04 (D:657-800)
4a: CATH_3ez5A02 (A:491-605)
4b: CATH_3ez5D02 (D:491-605)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.370, no name defined]
(99)
Bacillus stearothermophilus.
(2)
1a
3ez5A03
A:606-656,A:801-875
1b
3ez5D03
D:606-656,D:801-875
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
Bacillus stearothermophilus.
(2)
2a
3ez5D01
D:298-490
2b
3ez5A01
A:297-490
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
Bacillus stearothermophilus.
(2)
3a
3ez5A04
A:657-800
3b
3ez5D04
D:657-800
Architecture
:
Up-down Bundle
(3216)
Topology
:
Taq DNA Polymerase; Chain T, domain 4
(88)
Homologous Superfamily
:
Taq DNA Polymerase; Chain T, domain 4
(88)
Bacillus stearothermophilus.
(2)
4a
3ez5A02
A:491-605
4b
3ez5D02
D:491-605
[
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
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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(selected part)
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by Secondary Structure
by Atom (CPK)
by SCOP Domain
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by Exon
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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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)
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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") .
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") .
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