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1OYX
Biol. Unit 1
Info
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, 108)
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
21
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2
MSE
45
Mod. Amino Acid
SELENOMETHIONINE
3
SO4
42
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, 9)
Info
(mutated residues are only available for the asymmetric unit)
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, 27)
Info
All PROSITE Patterns/Profiles
1: MBT (A:206-306,B:206-306,A:314-413,B: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
27
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.
(no "Exon" information available for biological units yet)
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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