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Getting 'PROSITE' information from database.
2EX3
Biol. Unit 1
Info
Asym.Unit (760 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (132 KB)
Biol.Unit 3 (132 KB)
Biol.Unit 4 (132 KB)
Biol.Unit 5 (131 KB)
Biol.Unit 6 (132 KB)
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(1)
Title
:
BACTERIOPHAGE PHI29 DNA POLYMERASE BOUND TO TERMINAL PROTEIN
Authors
:
S. Kamtekar, A. J. Berman, J. Wang, M. De Vega, L. Blanco, M. Salas, T. A.
Date
:
07 Nov 05 (Deposition) - 14 Mar 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Dna Polymerase: Protein Primer Complex, Transferase-Replication Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Kamtekar, A. J. Berman, J. Wang, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
The Phi29 Dna Polymerase:Protein-Primer Structure Suggests Model For The Initiation To Elongation Transition
Embo J. V. 25 1335 2006
[
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: LEAD (II) ION (PBa)
1b: LEAD (II) ION (PBb)
1c: LEAD (II) ION (PBc)
1d: LEAD (II) ION (PBd)
1e: LEAD (II) ION (PBe)
1f: LEAD (II) ION (PBf)
1g: LEAD (II) ION (PBg)
1h: LEAD (II) ION (PBh)
1i: LEAD (II) ION (PBi)
1j: LEAD (II) ION (PBj)
1k: LEAD (II) ION (PBk)
1l: LEAD (II) ION (PBl)
1m: LEAD (II) ION (PBm)
1n: LEAD (II) ION (PBn)
1o: LEAD (II) ION (PBo)
1p: LEAD (II) ION (PBp)
2a: (UNKa)
2aa: (UNKaa)
2ab: (UNKab)
2ac: (UNKac)
2ad: (UNKad)
2ae: (UNKae)
2af: (UNKaf)
2ag: (UNKag)
2ah: (UNKah)
2ai: (UNKai)
2aj: (UNKaj)
2ak: (UNKak)
2al: (UNKal)
2am: (UNKam)
2an: (UNKan)
2ao: (UNKao)
2ap: (UNKap)
2aq: (UNKaq)
2ar: (UNKar)
2as: (UNKas)
2at: (UNKat)
2au: (UNKau)
2av: (UNKav)
2aw: (UNKaw)
2ax: (UNKax)
2ay: (UNKay)
2az: (UNKaz)
2b: (UNKb)
2ba: (UNKba)
2bb: (UNKbb)
2bc: (UNKbc)
2bd: (UNKbd)
2be: (UNKbe)
2bf: (UNKbf)
2bg: (UNKbg)
2bh: (UNKbh)
2bi: (UNKbi)
2bj: (UNKbj)
2bk: (UNKbk)
2bl: (UNKbl)
2bm: (UNKbm)
2bn: (UNKbn)
2bo: (UNKbo)
2bp: (UNKbp)
2bq: (UNKbq)
2br: (UNKbr)
2bs: (UNKbs)
2bt: (UNKbt)
2bu: (UNKbu)
2bv: (UNKbv)
2bw: (UNKbw)
2bx: (UNKbx)
2by: (UNKby)
2bz: (UNKbz)
2c: (UNKc)
2ca: (UNKca)
2cb: (UNKcb)
2cc: (UNKcc)
2cd: (UNKcd)
2ce: (UNKce)
2cf: (UNKcf)
2cg: (UNKcg)
2ch: (UNKch)
2ci: (UNKci)
2cj: (UNKcj)
2ck: (UNKck)
2cl: (UNKcl)
2cm: (UNKcm)
2cn: (UNKcn)
2co: (UNKco)
2cp: (UNKcp)
2cq: (UNKcq)
2cr: (UNKcr)
2cs: (UNKcs)
2ct: (UNKct)
2cu: (UNKcu)
2cv: (UNKcv)
2cw: (UNKcw)
2cx: (UNKcx)
2cy: (UNKcy)
2cz: (UNKcz)
2d: (UNKd)
2da: (UNKda)
2db: (UNKdb)
2dc: (UNKdc)
2dd: (UNKdd)
2de: (UNKde)
2df: (UNKdf)
2dg: (UNKdg)
2dh: (UNKdh)
2di: (UNKdi)
2dj: (UNKdj)
2dk: (UNKdk)
2dl: (UNKdl)
2dm: (UNKdm)
2dn: (UNKdn)
2do: (UNKdo)
2dp: (UNKdp)
2dq: (UNKdq)
2dr: (UNKdr)
2ds: (UNKds)
2dt: (UNKdt)
2du: (UNKdu)
2dv: (UNKdv)
2dw: (UNKdw)
2dx: (UNKdx)
2dy: (UNKdy)
2dz: (UNKdz)
2e: (UNKe)
2ea: (UNKea)
2eb: (UNKeb)
2ec: (UNKec)
2ed: (UNKed)
2ee: (UNKee)
2ef: (UNKef)
2eg: (UNKeg)
2eh: (UNKeh)
2ei: (UNKei)
2ej: (UNKej)
2ek: (UNKek)
2el: (UNKel)
2em: (UNKem)
2en: (UNKen)
2eo: (UNKeo)
2ep: (UNKep)
2eq: (UNKeq)
2er: (UNKer)
2es: (UNKes)
2et: (UNKet)
2eu: (UNKeu)
2ev: (UNKev)
2ew: (UNKew)
2ex: (UNKex)
2ey: (UNKey)
2ez: (UNKez)
2f: (UNKf)
2fa: (UNKfa)
2fb: (UNKfb)
2fc: (UNKfc)
2fd: (UNKfd)
2fe: (UNKfe)
2ff: (UNKff)
2fg: (UNKfg)
2fh: (UNKfh)
2fi: (UNKfi)
2fj: (UNKfj)
2fk: (UNKfk)
2fl: (UNKfl)
2fm: (UNKfm)
2fn: (UNKfn)
2fo: (UNKfo)
2fp: (UNKfp)
2fq: (UNKfq)
2fr: (UNKfr)
2fs: (UNKfs)
2ft: (UNKft)
2fu: (UNKfu)
2fv: (UNKfv)
2fw: (UNKfw)
2fx: (UNKfx)
2fy: (UNKfy)
2fz: (UNKfz)
2g: (UNKg)
2ga: (UNKga)
2gb: (UNKgb)
2gc: (UNKgc)
2gd: (UNKgd)
2ge: (UNKge)
2gf: (UNKgf)
2gg: (UNKgg)
2gh: (UNKgh)
2gi: (UNKgi)
2gj: (UNKgj)
2gk: (UNKgk)
2gl: (UNKgl)
2gm: (UNKgm)
2gn: (UNKgn)
2go: (UNKgo)
2gp: (UNKgp)
2gq: (UNKgq)
2gr: (UNKgr)
2gs: (UNKgs)
2gt: (UNKgt)
2gu: (UNKgu)
2gv: (UNKgv)
2h: (UNKh)
2i: (UNKi)
2j: (UNKj)
2k: (UNKk)
2l: (UNKl)
2m: (UNKm)
2n: (UNKn)
2o: (UNKo)
2p: (UNKp)
2q: (UNKq)
2r: (UNKr)
2s: (UNKs)
2t: (UNKt)
2u: (UNKu)
2v: (UNKv)
2w: (UNKw)
2x: (UNKx)
2y: (UNKy)
2z: (UNKz)
View:
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Label:
Sorry, no Info available
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:169
BINDING SITE FOR RESIDUE PB A 701
2
AC2
SOFTWARE
GLU A:14 , ASP A:145 , TYR A:148 , ASP A:169
BINDING SITE FOR RESIDUE PB A 702
3
AC3
SOFTWARE
GLU A:221
BINDING SITE FOR RESIDUE PB A 703
[
close Site info
]
SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_DPOL_BPPH2_001 (A176R, chain A, )
2: VAR_DPOL_BPPH2_002 (A355V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DPOL_BPPH2_001
*
A
176
R
DPOL_BPPH2
---
---
A
A
176
R
2
UniProt
VAR_DPOL_BPPH2_002
*
A
355
V
DPOL_BPPH2
---
---
A
A
355
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:454-462)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_B
PS00116
DNA polymerase family B signature.
DPOL_BPPH2
454-462
1
A:454-462
-
-
-
-
-
[
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]
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 18)
Info
All SCOP Domains
1a: SCOP_d2ex3b1 (B:71-259)
1b: SCOP_d2ex3d1 (D:71-259)
1c: SCOP_d2ex3f1 (F:71-259)
1d: SCOP_d2ex3h1 (H:71-259)
1e: SCOP_d2ex3j1 (J:71-259)
1f: SCOP_d2ex3l1 (L:71-259)
2a: SCOP_d2ex3a1 (A:6-187)
2b: SCOP_d2ex3c1 (C:6-187)
2c: SCOP_d2ex3e1 (E:6-187)
2d: SCOP_d2ex3g1 (G:6-187)
2e: SCOP_d2ex3i1 (I:6-187)
2f: SCOP_d2ex3k1 (K:6-187)
3a: SCOP_d2ex3a2 (A:188-575)
3b: SCOP_d2ex3c2 (C:188-575)
3c: SCOP_d2ex3e2 (E:188-575)
3d: SCOP_d2ex3g2 (G:188-575)
3e: SCOP_d2ex3i2 (I:188-575)
3f: SCOP_d2ex3k2 (K:188-575)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA terminal protein
(1)
Superfamily
:
DNA terminal protein
(1)
Family
:
DNA terminal protein
(1)
Protein domain
:
DNA terminal protein
(1)
Bacteriophage phi-29 [TaxId: 10756]
(1)
1a
d2ex3b1
B:71-259
1b
d2ex3d1
D:71-259
1c
d2ex3f1
F:71-259
1d
d2ex3h1
H:71-259
1e
d2ex3j1
J:71-259
1f
d2ex3l1
L:71-259
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 phi29 DNA polymerase
(8)
Bacteriophage phi-29 [TaxId: 10756]
(8)
2a
d2ex3a1
A:6-187
2b
d2ex3c1
C:6-187
2c
d2ex3e1
E:6-187
2d
d2ex3g1
G:6-187
2e
d2ex3i1
I:6-187
2f
d2ex3k1
K:6-187
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
:
phi29 DNA polymerase
(8)
Bacteriophage phi-29 [TaxId: 10756]
(8)
3a
d2ex3a2
A:188-575
3b
d2ex3c2
C:188-575
3c
d2ex3e2
E:188-575
3d
d2ex3g2
G:188-575
3e
d2ex3i2
I:188-575
3f
d2ex3k2
K:188-575
[
close SCOP info
]
CATH Domains
(6, 36)
Info
all CATH domains
1a: CATH_2ex3A01 (A:6-188)
1b: CATH_2ex3C01 (C:6-188)
1c: CATH_2ex3E01 (E:6-188)
1d: CATH_2ex3G01 (G:6-188)
1e: CATH_2ex3I01 (I:6-188)
1f: CATH_2ex3K01 (K:6-188)
2a: CATH_2ex3A03 (A:262-359)
2b: CATH_2ex3C03 (C:262-359)
2c: CATH_2ex3E03 (E:262-359)
2d: CATH_2ex3G03 (G:262-359)
2e: CATH_2ex3I03 (I:262-359)
2f: CATH_2ex3K03 (K:262-359)
3a: CATH_2ex3A02 (A:189-261,A:426-531)
3b: CATH_2ex3C02 (C:189-261,C:426-531)
3c: CATH_2ex3E02 (E:189-261,E:426-531)
3d: CATH_2ex3G02 (G:189-261,G:426-531)
3e: CATH_2ex3I02 (I:189-261,I:426-531)
3f: CATH_2ex3K02 (K:189-261,K:426-531)
4a: CATH_2ex3A05 (A:396-425)
4b: CATH_2ex3C05 (C:396-425)
4c: CATH_2ex3E05 (E:396-425)
4d: CATH_2ex3G05 (G:396-425)
4e: CATH_2ex3I05 (I:396-425)
4f: CATH_2ex3K05 (K:396-425)
5a: CATH_2ex3A06 (A:532-575)
5b: CATH_2ex3C06 (C:532-575)
5c: CATH_2ex3E06 (E:532-575)
5d: CATH_2ex3G06 (G:532-575)
5e: CATH_2ex3I06 (I:532-575)
5f: CATH_2ex3K06 (K:532-575)
6a: CATH_2ex3A04 (A:360-395)
6b: CATH_2ex3C04 (C:360-395)
6c: CATH_2ex3E04 (E:360-395)
6d: CATH_2ex3G04 (G:360-395)
6e: CATH_2ex3I04 (I:360-395)
6f: CATH_2ex3K04 (K:360-395)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
1a
2ex3A01
A:6-188
1b
2ex3C01
C:6-188
1c
2ex3E01
E:6-188
1d
2ex3G01
G:6-188
1e
2ex3I01
I:6-188
1f
2ex3K01
K:6-188
Topology
:
TPR 1 domain of DNA polymerase
(8)
Homologous Superfamily
:
TPR 1 domain of DNA polymerase
(8)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
2a
2ex3A03
A:262-359
2b
2ex3C03
C:262-359
2c
2ex3E03
E:262-359
2d
2ex3G03
G:262-359
2e
2ex3I03
I:262-359
2f
2ex3K03
K:262-359
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Palm domain of DNA polymerase
(8)
Homologous Superfamily
:
Palm domain of DNA polymerase
(8)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
3a
2ex3A02
A:189-261,A:426-531
3b
2ex3C02
C:189-261,C:426-531
3c
2ex3E02
E:189-261,E:426-531
3d
2ex3G02
G:189-261,G:426-531
3e
2ex3I02
I:189-261,I:426-531
3f
2ex3K02
K:189-261,K:426-531
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Rhinovirus 14, subunit 4
(101)
Homologous Superfamily
:
DNA polymerase; domain 5
(8)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
4a
2ex3A05
A:396-425
4b
2ex3C05
C:396-425
4c
2ex3E05
E:396-425
4d
2ex3G05
G:396-425
4e
2ex3I05
I:396-425
4f
2ex3K05
K:396-425
Homologous Superfamily
:
DNA polymerase; domain 6
(10)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
5a
2ex3A06
A:532-575
5b
2ex3C06
C:532-575
5c
2ex3E06
E:532-575
5d
2ex3G06
G:532-575
5e
2ex3I06
I:532-575
5f
2ex3K06
K:532-575
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
Bacillus phage phi29. Organism_taxid: 10756.
(2)
6a
2ex3A04
A:360-395
6b
2ex3C04
C:360-395
6c
2ex3E04
E:360-395
6d
2ex3G04
G:360-395
6e
2ex3I04
I:360-395
6f
2ex3K04
K:360-395
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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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
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show SS bonds with a radius of 100 units (=0.4Å)
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