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1R6Z
Biol. Unit 4
Info
Asym.Unit (229 KB)
Biol.Unit 1 (224 KB)
Biol.Unit 2 (78 KB)
Biol.Unit 3 (78 KB)
Biol.Unit 4 (78 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF THE ARGONAUTE2 PAZ DOMAIN (AS A MBP FUSION)
Authors
:
J. J. Song, J. Liu, N. H. Tolia, J. Schneiderman, S. K. Smith, R. A. Martie G. J. Hannon, L. Joshua-Tor
Date
:
17 Oct 03 (Deposition) - 13 Jan 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,P,Z
Biol. Unit 1: A,P,Z (1x)
Biol. Unit 2: P (1x)
Biol. Unit 3: A (1x)
Biol. Unit 4: Z (1x)
Keywords
:
Deviant Ob Fold, Rnai, Gene Regulation
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. J. Song, J. Liu, N. H. Tolia, J. Schneiderman, S. K. Smith, R. A. Martienssen, G. J. Hannon, L. Joshua-Tor
The Crystal Structure Of The Argonaute2 Paz Domain Reveals An Rna Binding Motif In Rnai Effector Complexes.
Nat. Struct. Biol. V. 10 1026 2003
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: MALTOSE (MALa)
1b: MALTOSE (MALb)
1c: MALTOSE (MALc)
2a: NICKEL (II) ION (NIa)
2b: NICKEL (II) ION (NIb)
2c: NICKEL (II) ION (NIc)
2d: NICKEL (II) ION (NId)
2e: NICKEL (II) ION (NIe)
2f: NICKEL (II) ION (NIf)
2g: NICKEL (II) ION (NIg)
2h: NICKEL (II) ION (NIh)
2i: NICKEL (II) ION (NIi)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MAL
1
Ligand/Ion
MALTOSE
2
NI
-1
Ligand/Ion
NICKEL (II) ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP Z:13 , LYS Z:14 , TRP Z:61 , ALA Z:62 , ASP Z:64 , ARG Z:65 , GLU Z:110 , GLU Z:152 , PRO Z:153 , TYR Z:154 , TRP Z:229 , TRP Z:339
BINDING SITE FOR RESIDUE MAL Z 727
2
AC4
SOFTWARE
HIS P:671 , ASP P:672 , HIS Z:595
BINDING SITE FOR RESIDUE NI P 728
3
AC6
SOFTWARE
HIS A:595 , HIS Z:671 , ASP Z:672
BINDING SITE FOR RESIDUE NI Z 728
4
AC7
SOFTWARE
HIS Z:38 , NI Z:730
BINDING SITE FOR RESIDUE NI Z 729
5
BC3
SOFTWARE
HIS Z:38 , NI Z:729
BINDING SITE FOR RESIDUE NI Z 730
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SBP_BACTERIAL_1 (Z:106-123)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SBP_BACTERIAL_1
PS01037
Bacterial extracellular solute-binding proteins, family 1 signature.
MALE_ECO57
133-150
1
-
-
Z:106-123
MALE_ECOLI
133-150
1
-
-
Z:106-123
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1r6za1 (A:591-716)
1b: SCOP_d1r6zp1 (P:591-717)
1c: SCOP_d1r6zz1 (Z:591-719)
2a: SCOP_d1r6za2 (A:1-371)
2b: SCOP_d1r6zp2 (P:1-371)
2c: SCOP_d1r6zz2 (Z:2-371)
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)
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)
Protein Domains
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)
(
)
Organisms
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)
(
)
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
PAZ domain
(15)
Family
:
PAZ domain
(15)
Protein domain
:
Argonaute 2
(4)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(4)
1a
d1r6za1
A:591-716
1b
d1r6zp1
P:591-717
1c
d1r6zz1
Z:591-719
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
D-maltodextrin-binding protein, MBP
(70)
Escherichia coli [TaxId: 562]
(60)
2a
d1r6za2
A:1-371
2b
d1r6zp2
P:1-371
2c
d1r6zz2
Z:2-371
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CATH Domains
(2, 9)
Info
all CATH domains
1a: CATH_1r6zA01 (A:1-110,A:257-330)
1b: CATH_1r6zZ01 (Z:2-111,Z:255-330)
1c: CATH_1r6zP01 (P:1-111,P:255-330)
1d: CATH_1r6zP02 (P:112-254,P:331-371)
1e: CATH_1r6zZ02 (Z:112-254,Z:331-371)
1f: CATH_1r6zA02 (A:111-256,A:331-371)
2a: CATH_1r6zA03 (A:591-716)
2b: CATH_1r6zP03 (P:591-717)
2c: CATH_1r6zZ03 (Z:591-719)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
, fruit fly (Escherichia coli, drosophila melanogaster)
(1)
1a
1r6zA01
A:1-110,A:257-330
1b
1r6zZ01
Z:2-111,Z:255-330
1c
1r6zP01
P:1-111,P:255-330
1d
1r6zP02
P:112-254,P:331-371
1e
1r6zZ02
Z:112-254,Z:331-371
1f
1r6zA02
A:111-256,A:331-371
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
paz domain
(7)
Homologous Superfamily
:
paz domain
(7)
, fruit fly (Escherichia coli, drosophila melanogaster)
(1)
2a
1r6zA03
A:591-716
2b
1r6zP03
P:591-717
2c
1r6zZ03
Z:591-719
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Pfam Domains
(0, 0)
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Chain Z
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (229 KB)
Header - Asym.Unit
Biol.Unit 1 (224 KB)
Header - Biol.Unit 1
Biol.Unit 2 (78 KB)
Header - Biol.Unit 2
Biol.Unit 3 (78 KB)
Header - Biol.Unit 3
Biol.Unit 4 (78 KB)
Header - Biol.Unit 4
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