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1OYX
Asym. Unit
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Asym.Unit (177 KB)
Biol.Unit 1 (499 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 3-MBT REPEATS OF LETHAL (3) MALIGNANT BRAIN TUMOR (SELENO-MET) AT 1.85 ANGSTROM
Authors
:
W. K. Wang, V. Tereshko, P. Boccuni, D. Macgrogan, S. D. Nimer, D. J. Patel
Date
:
07 Apr 03 (Deposition) - 19 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (3x)
Keywords
:
Propeller, Transcription Repressor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. K. Wang, V. Tereshko, P. Boccuni, D. Macgrogan, S. D. Nimer, D. J. Patel
Malignant Brain Tumor Repeats: A Three-Leaved Propeller Architecture With Ligand/Peptide Binding Pockets.
Structure V. 11 775 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 36)
Info
All Hetero Components
1a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
1b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
1c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
1d: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESd)
1e: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESe)
1f: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESf)
1g: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESg)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MES
7
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2
MSE
15
Mod. Amino Acid
SELENOMETHIONINE
3
SO4
14
Ligand/Ion
SULFATE ION
[
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]
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
TYR B:275 , SER B:276 , HIS B:279 , LYS B:307
BINDING SITE FOR RESIDUE SO4 B 2001
02
AC2
SOFTWARE
PRO A:446 , TYR C:275 , SER C:276 , HIS C:279 , LYS C:307
BINDING SITE FOR RESIDUE SO4 C 2002
03
AC3
SOFTWARE
ARG C:356 , TRP C:389 , CYS C:390 , SER C:394 , TYR C:396 , ARG C:444 , ASP C:495
BINDING SITE FOR RESIDUE SO4 C 2003
04
AC4
SOFTWARE
HIS B:482 , ASP B:484 , GLY B:485
BINDING SITE FOR RESIDUE SO4 B 2004
05
AC5
SOFTWARE
HIS A:482 , GLY A:485
BINDING SITE FOR RESIDUE SO4 A 2005
06
AC6
SOFTWARE
LYS C:235 , SER C:315 , TRP C:316 , SER C:317
BINDING SITE FOR RESIDUE SO4 C 2006
07
AC7
SOFTWARE
LYS C:298 , LYS C:330 , HIS C:338
BINDING SITE FOR RESIDUE SO4 C 2007
08
AC8
SOFTWARE
LYS A:235 , GLU A:297 , SER A:315 , TRP A:316 , SER A:317
BINDING SITE FOR RESIDUE SO4 A 2008
09
AC9
SOFTWARE
LYS A:442 , SER B:487 , HIS B:488
BINDING SITE FOR RESIDUE SO4 B 2009
10
BC1
SOFTWARE
PRO A:329 , LYS A:330 , HIS A:331
BINDING SITE FOR RESIDUE SO4 A 2010
11
BC2
SOFTWARE
ARG B:460 , HIS B:498 , HOH B:2027 , HOH B:2106 , HOH B:2152
BINDING SITE FOR RESIDUE SO4 B 2011
12
BC3
SOFTWARE
ARG A:460 , HIS A:498
BINDING SITE FOR RESIDUE SO4 A 2012
13
BC4
SOFTWARE
TYR A:490 , HOH A:2097 , PRO B:221 , VAL B:222 , HOH B:2210
BINDING SITE FOR RESIDUE SO4 B 2013
14
BC5
SOFTWARE
LYS B:235 , SER B:315 , TRP B:316 , SER B:317 , HOH B:2142
BINDING SITE FOR RESIDUE SO4 B 2014
15
BC6
SOFTWARE
PHE A:256 , PHE A:272 , TYR A:275 , SER A:276 , HIS A:279 , LYS A:307
BINDING SITE FOR RESIDUE MES A 1011
16
BC7
SOFTWARE
ASP A:355 , ASN A:358 , CYS A:363 , PHE A:379 , TRP A:382 , TYR A:386
BINDING SITE FOR RESIDUE MES A 1012
17
BC8
SOFTWARE
PHE B:256 , PHE B:272 , HIS B:279
BINDING SITE FOR RESIDUE MES B 1021
18
BC9
SOFTWARE
ASP B:355 , ASN B:358 , CYS B:363 , PHE B:379 , TRP B:382 , TYR B:386 , HOH C:2180
BINDING SITE FOR RESIDUE MES B 1022
19
CC1
SOFTWARE
ASP B:459 , ARG B:461 , PHE B:483 , TRP B:486
BINDING SITE FOR RESIDUE MES B 1023
20
CC2
SOFTWARE
PHE C:256 , TYR C:275 , HIS C:279
BINDING SITE FOR RESIDUE MES C 1031
21
CC3
SOFTWARE
ASP C:355 , ASN C:358 , PHE C:379 , TRP C:382 , TYR C:386
BINDING SITE FOR RESIDUE MES C 1032
[
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SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_051098 (I479M, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051098
I
479
M
LMBL1_HUMAN
Polymorphism
6017104
A/B/C
I
479
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 9)
Info
All PROSITE Patterns/Profiles
1: MBT (A:206-306,B:206-306,C:206-306|A:31...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MBT
PS51079
MBT repeat profile.
LMBL1_HUMAN
206-306
314-413
422-517
9
A:206-306
B:206-306
C:206-306
A:314-413
B:314-413
C:314-413
A:422-517
B:422-517
C:422-517
[
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Exons
(0, 0)
Info
All Exons
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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
(1, 9)
Info
All SCOP Domains
1a: SCOP_d1oyxa1 (A:206-313)
1b: SCOP_d1oyxa2 (A:314-421)
1c: SCOP_d1oyxa3 (A:422-518)
1d: SCOP_d1oyxb1 (B:206-313)
1e: SCOP_d1oyxb2 (B:314-421)
1f: SCOP_d1oyxb3 (B:422-518)
1g: SCOP_d1oyxc1 (C:206-313)
1h: SCOP_d1oyxc2 (C:314-421)
1i: SCOP_d1oyxc3 (C:422-518)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
Tudor/PWWP/MBT
(72)
Family
:
MBT repeat
(8)
Protein domain
:
Lethal(3)malignant brain tumor-like protein
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1oyxa1
A:206-313
1b
d1oyxa2
A:314-421
1c
d1oyxa3
A:422-518
1d
d1oyxb1
B:206-313
1e
d1oyxb2
B:314-421
1f
d1oyxb3
B:422-518
1g
d1oyxc1
C:206-313
1h
d1oyxc2
C:314-421
1i
d1oyxc3
C:422-518
[
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]
CATH Domains
(1, 9)
Info
all CATH domains
1a: CATH_1oyxA02 (A:235-338)
1b: CATH_1oyxA03 (A:339-446)
1c: CATH_1oyxB03 (B:339-446)
1d: CATH_1oyxC03 (C:339-446)
1e: CATH_1oyxB02 (B:235-338)
1f: CATH_1oyxC02 (C:235-338)
1g: CATH_1oyxA01 (A:206-234,A:447-518)
1h: CATH_1oyxB01 (B:206-234,B:447-518)
1i: CATH_1oyxC01 (C:206-234,C:447-518)
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)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
SH3 type barrels.
(648)
Homologous Superfamily
:
[code=2.30.30.160, no name defined]
(35)
Human (Homo sapiens)
(27)
1a
1oyxA02
A:235-338
1b
1oyxA03
A:339-446
1c
1oyxB03
B:339-446
1d
1oyxC03
C:339-446
1e
1oyxB02
B:235-338
1f
1oyxC02
C:235-338
1g
1oyxA01
A:206-234,A:447-518
1h
1oyxB01
B:206-234,B:447-518
1i
1oyxC01
C:206-234,C:447-518
[
close CATH info
]
Pfam Domains
(1, 9)
Info
all PFAM domains
1a: PFAM_MBT_1oyxC01 (C:453-518)
1b: PFAM_MBT_1oyxC02 (C:453-518)
1c: PFAM_MBT_1oyxC03 (C:453-518)
1d: PFAM_MBT_1oyxC04 (C:453-518)
1e: PFAM_MBT_1oyxC05 (C:453-518)
1f: PFAM_MBT_1oyxC06 (C:453-518)
1g: PFAM_MBT_1oyxC07 (C:453-518)
1h: PFAM_MBT_1oyxC08 (C:453-518)
1i: PFAM_MBT_1oyxC09 (C:453-518)
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Clans
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(
)
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(
)
Organisms
(
)
(
)
Clan
:
Tudor
(88)
Family
:
MBT
(24)
Homo sapiens (Human)
(20)
1a
MBT-1oyxC01
C:453-518
1b
MBT-1oyxC02
C:453-518
1c
MBT-1oyxC03
C:453-518
1d
MBT-1oyxC04
C:453-518
1e
MBT-1oyxC05
C:453-518
1f
MBT-1oyxC06
C:453-518
1g
MBT-1oyxC07
C:453-518
1h
MBT-1oyxC08
C:453-518
1i
MBT-1oyxC09
C:453-518
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