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1M8V
Asym. Unit
Info
Asym.Unit (198 KB)
Biol.Unit 1 (191 KB)
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(1)
Title
:
STRUCTURE OF PYROCOCCUS ABYSSII SM PROTEIN IN COMPLEX WITH A URIDINE HEPTAMER
Authors
:
S. Thore, C. Mayer, C. Sauter, S. Weeks, D. Suck
Date
:
26 Jul 02 (Deposition) - 11 Feb 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U (1x)
Keywords
:
Protein-Rna Complex, Sm Protein, Rna Binding Protein/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Thore, C. Mayer, C. Sauter, S. Weeks, D. Suck
Crystal Structure Of Pyrococcus Abyssii Sm Core And Its Complex With Rna: Common Features Of Rna-Binding In Archaea And Eukarya
J. Biol. Chem. V. 278 1239 2003
(for further references see the
PDB file header
)
[
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]
Hetero Components
(2, 21)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
2a: URIDINE-5'-MONOPHOSPHATE (Ua)
2b: URIDINE-5'-MONOPHOSPHATE (Ub)
2c: URIDINE-5'-MONOPHOSPHATE (Uc)
2d: URIDINE-5'-MONOPHOSPHATE (Ud)
2e: URIDINE-5'-MONOPHOSPHATE (Ue)
2f: URIDINE-5'-MONOPHOSPHATE (Uf)
2g: URIDINE-5'-MONOPHOSPHATE (Ug)
2h: URIDINE-5'-MONOPHOSPHATE (Uh)
2i: URIDINE-5'-MONOPHOSPHATE (Ui)
2j: URIDINE-5'-MONOPHOSPHATE (Uj)
2k: URIDINE-5'-MONOPHOSPHATE (Uk)
2l: URIDINE-5'-MONOPHOSPHATE (Ul)
2m: URIDINE-5'-MONOPHOSPHATE (Um)
2n: URIDINE-5'-MONOPHOSPHATE (Un)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
7
Ligand/Ion
CALCIUM ION
2
U
14
Ligand/Ion
URIDINE-5'-MONOPHOSPHATE
[
close Hetero Component info
]
Sites
(21, 21)
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)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
U O:2 , U O:3 , U O:4 , U O:5 , U O:6
BINDING SITE FOR RESIDUE CA O 310
02
AC2
SOFTWARE
U T:2 , U T:3 , U T:5
BINDING SITE FOR RESIDUE CA T 320
03
AC3
SOFTWARE
U P:2 , U P:3 , U P:5 , U P:6
BINDING SITE FOR RESIDUE CA P 330
04
AC4
SOFTWARE
U S:2 , U S:3 , U S:5 , U S:6
BINDING SITE FOR RESIDUE CA S 340
05
AC5
SOFTWARE
U U:2 , U U:3 , U U:5 , U U:6
BINDING SITE FOR RESIDUE CA U 370
06
AC6
SOFTWARE
U Q:2 , U Q:3 , U Q:5 , U Q:6
BINDING SITE FOR RESIDUE CA Q 380
07
AC7
SOFTWARE
U R:2 , U R:3 , U R:5 , U R:6
BINDING SITE FOR RESIDUE CA R 390
08
AC8
SOFTWARE
HIS A:137 , ASN A:139 , ARG A:163 , GLY A:164 , ASP A:165 , ARG B:263 , U B:411 , U G:416 , LEU G:738
BINDING SITE FOR RESIDUE U A 410
09
AC9
SOFTWARE
LEU A:138 , U A:410 , HIS B:237 , ASN B:239 , ARG B:263 , GLY B:264 , ASP B:265 , HOH C:120 , U C:412
BINDING SITE FOR RESIDUE U B 411
10
BC1
SOFTWARE
ILE B:236 , LEU B:238 , U B:411 , HOH C:120 , HIS C:337 , ASN C:339 , ARG C:363 , GLY C:364 , ASP C:365 , ARG D:463 , U D:476
BINDING SITE FOR RESIDUE U C 412
11
BC2
SOFTWARE
HOH C:133 , LEU C:338 , U C:412 , HIS D:437 , ASN D:439 , ARG D:463 , GLY D:464 , ASP D:465 , U E:414 , ARG E:563
BINDING SITE FOR RESIDUE U D 476
12
BC3
SOFTWARE
HOH D:9 , HIS D:437 , LEU D:438 , U D:476 , ASN E:539 , ARG E:563 , ASP E:565 , U F:415 , ARG F:663
BINDING SITE FOR RESIDUE U E 414
13
BC4
SOFTWARE
HOH E:180 , U E:414 , HIS E:537 , LEU E:538 , HIS F:637 , ASN F:639 , ARG F:663 , GLY F:664 , ASP F:665 , U G:416 , ARG G:763
BINDING SITE FOR RESIDUE U F 415
14
BC5
SOFTWARE
U A:410 , U F:415 , LEU F:638 , HIS G:737 , ASN G:739 , ARG G:763 , ASP G:765
BINDING SITE FOR RESIDUE U G 416
15
BC6
SOFTWARE
HIS H:137 , ASN H:139 , ARG H:163 , ASP H:165 , ARG I:263 , U I:418 , U M:423 , LEU N:738
BINDING SITE FOR RESIDUE U H 417
16
BC7
SOFTWARE
LEU H:138 , U H:417 , HIS I:237 , ASN I:239 , ARG I:263 , ASP I:265 , ARG J:363 , U J:419
BINDING SITE FOR RESIDUE U I 418
17
BC8
SOFTWARE
LEU I:238 , U I:418 , HOH I:425 , ASN J:339 , ARG J:363 , GLY J:364 , ASP J:365 , ARG K:463 , U K:476
BINDING SITE FOR RESIDUE U J 419
18
BC9
SOFTWARE
HOH J:255 , LEU J:338 , U J:419 , HIS K:437 , ASN K:439 , ARG K:463 , GLY K:464 , ASP K:465 , U L:421 , ARG L:563
BINDING SITE FOR RESIDUE U K 476
19
CC1
SOFTWARE
HOH K:220 , HIS K:437 , LEU K:438 , U K:476 , HIS L:537 , ASN L:539 , ARG L:563 , ASP L:565 , U M:422 , ARG M:663
BINDING SITE FOR RESIDUE U L 421
20
CC2
SOFTWARE
U L:421 , LEU L:538 , HOH M:32 , U M:423 , HIS M:637 , ASN M:639 , ARG M:663 , ASP M:665
BINDING SITE FOR RESIDUE U M 422
21
CC3
SOFTWARE
U H:417 , U M:422 , LYS M:622 , LEU M:638 , ASP M:665 , HIS N:737 , ASN N:739 , ARG N:763 , ASP N:765
BINDING SITE FOR RESIDUE U M 423
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
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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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 14)
Info
All SCOP Domains
1a: SCOP_d1m8va_ (A:)
1b: SCOP_d1m8vb_ (B:)
1c: SCOP_d1m8vc_ (C:)
1d: SCOP_d1m8vd_ (D:)
1e: SCOP_d1m8ve_ (E:)
1f: SCOP_d1m8vf_ (F:)
1g: SCOP_d1m8vg_ (G:)
1h: SCOP_d1m8vh_ (H:)
1i: SCOP_d1m8vi_ (I:)
1j: SCOP_d1m8vj_ (J:)
1k: SCOP_d1m8vk_ (K:)
1l: SCOP_d1m8vl_ (L:)
1m: SCOP_d1m8vm_ (M:)
1n: SCOP_d1m8vn_ (N:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Sm-like fold
(103)
Superfamily
:
Sm-like ribonucleoproteins
(95)
Family
:
Sm motif of small nuclear ribonucleoproteins, SNRNP
(31)
Protein domain
:
Archaeal homoheptameric Sm protein
(13)
Pyrococcus abyssi [TaxId: 29292]
(2)
1a
d1m8va_
A:
1b
d1m8vb_
B:
1c
d1m8vc_
C:
1d
d1m8vd_
D:
1e
d1m8ve_
E:
1f
d1m8vf_
F:
1g
d1m8vg_
G:
1h
d1m8vh_
H:
1i
d1m8vi_
I:
1j
d1m8vj_
J:
1k
d1m8vk_
K:
1l
d1m8vl_
L:
1m
d1m8vm_
M:
1n
d1m8vn_
N:
[
close SCOP info
]
CATH Domains
(1, 14)
Info
all CATH domains
1a: CATH_1m8vB00 (B:203-273)
1b: CATH_1m8vF00 (F:603-673)
1c: CATH_1m8vG00 (G:703-773)
1d: CATH_1m8vH00 (H:103-173)
1e: CATH_1m8vI00 (I:203-273)
1f: CATH_1m8vJ00 (J:303-373)
1g: CATH_1m8vK00 (K:403-473)
1h: CATH_1m8vL00 (L:503-573)
1i: CATH_1m8vM00 (M:603-673)
1j: CATH_1m8vN00 (N:703-773)
1k: CATH_1m8vA00 (A:102-173)
1l: CATH_1m8vC00 (C:303-373)
1m: CATH_1m8vD00 (D:403-473)
1n: CATH_1m8vE00 (E:503-573)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
SH3 type barrels.
(648)
Homologous Superfamily
:
[code=2.30.30.100, no name defined]
(40)
[unclassified]
(3)
1a
1m8vB00
B:203-273
1b
1m8vF00
F:603-673
1c
1m8vG00
G:703-773
1d
1m8vH00
H:103-173
1e
1m8vI00
I:203-273
1f
1m8vJ00
J:303-373
1g
1m8vK00
K:403-473
1h
1m8vL00
L:503-573
1i
1m8vM00
M:603-673
1j
1m8vN00
N:703-773
1k
1m8vA00
A:102-173
1l
1m8vC00
C:303-373
1m
1m8vD00
D:403-473
1n
1m8vE00
E:503-573
[
close CATH info
]
Pfam Domains
(1, 14)
Info
all PFAM domains
1a: PFAM_LSM_1m8vN01 (N:707-772)
1b: PFAM_LSM_1m8vN02 (N:707-772)
1c: PFAM_LSM_1m8vN03 (N:707-772)
1d: PFAM_LSM_1m8vN04 (N:707-772)
1e: PFAM_LSM_1m8vN05 (N:707-772)
1f: PFAM_LSM_1m8vN06 (N:707-772)
1g: PFAM_LSM_1m8vN07 (N:707-772)
1h: PFAM_LSM_1m8vN08 (N:707-772)
1i: PFAM_LSM_1m8vN09 (N:707-772)
1j: PFAM_LSM_1m8vN10 (N:707-772)
1k: PFAM_LSM_1m8vN11 (N:707-772)
1l: PFAM_LSM_1m8vN12 (N:707-772)
1m: PFAM_LSM_1m8vN13 (N:707-772)
1n: PFAM_LSM_1m8vN14 (N:707-772)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Sm-like
(17)
Family
:
LSM
(13)
Pyrococcus abyssi (strain GE5 / Orsay)
(1)
1a
LSM-1m8vN01
N:707-772
1b
LSM-1m8vN02
N:707-772
1c
LSM-1m8vN03
N:707-772
1d
LSM-1m8vN04
N:707-772
1e
LSM-1m8vN05
N:707-772
1f
LSM-1m8vN06
N:707-772
1g
LSM-1m8vN07
N:707-772
1h
LSM-1m8vN08
N:707-772
1i
LSM-1m8vN09
N:707-772
1j
LSM-1m8vN10
N:707-772
1k
LSM-1m8vN11
N:707-772
1l
LSM-1m8vN12
N:707-772
1m
LSM-1m8vN13
N:707-772
1n
LSM-1m8vN14
N:707-772
[
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]
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Asym.Unit (198 KB)
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