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1S32
Asym. Unit
Info
Asym.Unit (281 KB)
Biol.Unit 1 (272 KB)
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(1)
Title
:
MOLECULAR RECOGNITION OF THE NUCLEOSOMAL 'SUPERGROOVE'
Authors
:
R. S. Edayathumangalam, P. Weyermann, J. M. Gottesfeld, P. B. Dervan, K
Date
:
12 Jan 04 (Deposition) - 11 May 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Nucleosome Core Particle (Ncp), Pyrrole-Imidazole (Py-Im) Hairpin Polyamide, Clamp, Nucleosome Dynamics, Structural Protein-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. S. Edayathumangalam, P. Weyermann, J. M. Gottesfeld, P. B. Dervan, K. Luger
Molecular Recognition Of The Nucleosomal 'Supergroove'
Proc. Natl. Acad. Sci. Usa V. 101 6864 2004
[
close entry info
]
Hetero Components
(8, 41)
Info
All Hetero Components
1a: GAMMA-AMINO-BUTANOIC ACID (ABUa)
1b: GAMMA-AMINO-BUTANOIC ACID (ABUb)
2a: BETA-ALANINE (BALa)
2b: BETA-ALANINE (BALb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
4a: 3-AMINO-(DIMETHYLPROPYLAMINE) (DIBa)
4b: 3-AMINO-(DIMETHYLPROPYLAMINE) (DIBb)
5a: 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARB... (IMTa)
5b: 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARB... (IMTb)
5c: 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARB... (IMTc)
5d: 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARB... (IMTd)
6a: MANGANESE (II) ION (MNa)
6b: MANGANESE (II) ION (MNb)
6c: MANGANESE (II) ION (MNc)
6d: MANGANESE (II) ION (MNd)
6e: MANGANESE (II) ION (MNe)
6f: MANGANESE (II) ION (MNf)
6g: MANGANESE (II) ION (MNg)
6h: MANGANESE (II) ION (MNh)
6i: MANGANESE (II) ION (MNi)
6j: MANGANESE (II) ION (MNj)
6k: MANGANESE (II) ION (MNk)
6l: MANGANESE (II) ION (MNl)
6m: MANGANESE (II) ION (MNm)
6n: MANGANESE (II) ION (MNn)
7a: 2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACET... (OGGa)
8a: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBa)
8b: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBb)
8c: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBc)
8d: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBd)
8e: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBe)
8f: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBf)
8g: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBg)
8h: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBh)
8i: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBi)
8j: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBj)
8k: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBk)
8l: 4-AMINO-(1-METHYLPYRROLE)-2-CARBOX... (PYBl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ABU
2
Ligand/Ion
GAMMA-AMINO-BUTANOIC ACID
2
BAL
2
Ligand/Ion
BETA-ALANINE
3
CL
4
Ligand/Ion
CHLORIDE ION
4
DIB
2
Ligand/Ion
3-AMINO-(DIMETHYLPROPYLAMINE)
5
IMT
4
Ligand/Ion
4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID
6
MN
14
Ligand/Ion
MANGANESE (II) ION
7
OGG
1
Ligand/Ion
2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE
8
PYB
12
Ligand/Ion
4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(41, 41)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL D:1245 , ASP E:677 , HOH E:3391 , HOH E:3393 , HOH E:3394 , HOH F:3392
BINDING SITE FOR RESIDUE MN E 2001
02
AC2
SOFTWARE
HOH I:3396 , DG J:246 , HOH J:3395 , HOH J:3397 , HOH J:3398 , HOH J:3399
BINDING SITE FOR RESIDUE MN J 2002
03
AC3
SOFTWARE
DG I:70 , DG I:71 , HOH I:3400
BINDING SITE FOR RESIDUE MN I 2003
04
AC4
SOFTWARE
DG I:134 , HOH I:3401 , HOH I:3402 , HOH I:3403
BINDING SITE FOR RESIDUE MN I 2004
05
AC5
SOFTWARE
DG J:280 , HOH J:3641
BINDING SITE FOR RESIDUE MN J 2005
06
AC6
SOFTWARE
DG I:100 , HOH I:3526 , HOH I:3832
BINDING SITE FOR RESIDUE MN I 2006
07
AC7
SOFTWARE
DG I:39 , DG I:40 , HOH I:3153
BINDING SITE FOR RESIDUE MN I 2007
08
AC8
SOFTWARE
DT J:266 , DG J:267 , HOH J:3047 , HOH J:3411
BINDING SITE FOR RESIDUE MN J 2008
09
AC9
SOFTWARE
DG I:121
BINDING SITE FOR RESIDUE MN I 2009
10
BC1
SOFTWARE
DG J:217 , HOH J:3491
BINDING SITE FOR RESIDUE MN J 2010
11
BC2
SOFTWARE
DG J:227
BINDING SITE FOR RESIDUE MN J 2011
12
BC3
SOFTWARE
HOH I:3821 , HOH J:3295 , HOH J:3820 , HOH J:3833
BINDING SITE FOR RESIDUE MN I 2012
13
BC4
SOFTWARE
DG J:185 , DG J:186 , HOH J:3499
BINDING SITE FOR RESIDUE MN J 2013
14
BC5
SOFTWARE
DG I:137 , DG I:138 , HOH I:3233
BINDING SITE FOR RESIDUE MN I 2014
15
BC6
SOFTWARE
PRO E:721 , LYS E:722
BINDING SITE FOR RESIDUE CL E 2015
16
BC7
SOFTWARE
GLY G:1044 , ALA G:1045 , GLY G:1046 , ALA G:1047 , THR H:1487 , SER H:1488
BINDING SITE FOR RESIDUE CL G 2016
17
BC8
SOFTWARE
PRO A:521 , LYS A:522
BINDING SITE FOR RESIDUE CL A 2017
18
BC9
SOFTWARE
GLY C:846 , ALA C:847 , THR D:1287 , SER D:1288
BINDING SITE FOR RESIDUE CL D 2018
19
CC1
SOFTWARE
DG I:31 , DT I:32 , PYB I:1602 , PYB I:1608 , PYB I:1609
BINDING SITE FOR RESIDUE IMT I 1601
20
CC2
SOFTWARE
DT I:32 , DG I:33 , IMT I:1601 , IMT I:1603 , PYB I:1607 , PYB I:1608
BINDING SITE FOR RESIDUE PYB I 1602
21
CC3
SOFTWARE
DG I:33 , DT I:34 , DA I:35 , PYB I:1602 , PYB I:1604
BINDING SITE FOR RESIDUE IMT I 1603
22
CC4
SOFTWARE
DT I:34 , DA I:35 , DT I:36 , IMT I:1603 , ABU I:1605 , PYB I:1606 , HOH I:3243
BINDING SITE FOR RESIDUE PYB I 1604
23
CC5
SOFTWARE
PYB I:1604 , PYB I:1606 , DA J:259 , DC J:260 , OGG J:1700
BINDING SITE FOR RESIDUE ABU I 1605
24
CC6
SOFTWARE
PYB I:1604 , ABU I:1605 , PYB I:1607 , DA J:259 , DC J:260 , DA J:261 , OGG J:1700
BINDING SITE FOR RESIDUE PYB I 1606
25
CC7
SOFTWARE
PYB I:1602 , PYB I:1606 , PYB I:1608 , DC J:260 , DA J:261
BINDING SITE FOR RESIDUE PYB I 1607
26
CC8
SOFTWARE
IMT I:1601 , PYB I:1602 , PYB I:1607 , PYB I:1609 , DA J:261 , DC J:262 , DT J:263
BINDING SITE FOR RESIDUE PYB I 1608
27
CC9
SOFTWARE
DG I:31 , IMT I:1601 , PYB I:1608 , BAL I:1610 , DC J:262 , DT J:263
BINDING SITE FOR RESIDUE PYB I 1609
28
DC1
SOFTWARE
DA I:30 , DG I:31 , PYB I:1609 , DIB I:1611 , DT J:263
BINDING SITE FOR RESIDUE BAL I 1610
29
DC2
SOFTWARE
DA I:29 , DA I:30 , BAL I:1610 , DT J:265 , DT J:266
BINDING SITE FOR RESIDUE DIB I 1611
30
DC3
SOFTWARE
PYB I:1622 , PYB I:1628 , PYB I:1629 , DT J:178
BINDING SITE FOR RESIDUE IMT I 1621
31
DC4
SOFTWARE
IMT I:1621 , IMT I:1623 , PYB I:1627 , PYB I:1628 , DT J:178 , DG J:179
BINDING SITE FOR RESIDUE PYB I 1622
32
DC5
SOFTWARE
PYB I:1622 , PYB I:1624 , PYB I:1627 , DG J:179 , DT J:180 , DA J:181
BINDING SITE FOR RESIDUE IMT I 1623
33
DC6
SOFTWARE
DA I:113 , IMT I:1623 , ABU I:1625 , PYB I:1626 , DT J:180 , DA J:181 , DT J:182
BINDING SITE FOR RESIDUE PYB I 1624
34
DC7
SOFTWARE
DA I:113 , PYB I:1624 , PYB I:1626 , DA J:181 , OGG J:1700
BINDING SITE FOR RESIDUE ABU I 1625
35
DC8
SOFTWARE
DA I:113 , DC I:114 , DA I:115 , PYB I:1624 , ABU I:1625 , PYB I:1627 , OGG J:1700
BINDING SITE FOR RESIDUE PYB I 1626
36
DC9
SOFTWARE
DC I:114 , DA I:115 , DC I:116 , PYB I:1622 , IMT I:1623 , PYB I:1626 , PYB I:1628
BINDING SITE FOR RESIDUE PYB I 1627
37
EC1
SOFTWARE
DA I:115 , DC I:116 , DT I:117 , IMT I:1621 , PYB I:1622 , PYB I:1627 , PYB I:1629
BINDING SITE FOR RESIDUE PYB I 1628
38
EC2
SOFTWARE
LYS G:1013 , DC I:116 , DT I:117 , DT I:118 , IMT I:1621 , PYB I:1628 , BAL I:1630 , DG J:177
BINDING SITE FOR RESIDUE PYB I 1629
39
EC3
SOFTWARE
ALA G:1014 , PYB I:1629 , DIB I:1631 , DA J:176 , DG J:177
BINDING SITE FOR RESIDUE BAL I 1630
40
EC4
SOFTWARE
DT I:119 , DT I:120 , BAL I:1630 , DA J:175 , DA J:176
BINDING SITE FOR RESIDUE DIB I 1631
41
EC5
SOFTWARE
DA I:113 , ABU I:1605 , PYB I:1606 , ABU I:1625 , PYB I:1626 , DA J:259
BINDING SITE FOR RESIDUE OGG J 1700
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036206 (E263Q, chain B/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036206
E
64
Q
H4_HUMAN
Unclassified
---
B
F
E
63
263
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H2A (C:821-827,G:1021-1027)
2: HISTONE_H3_2 (A:466-474,E:666-674)
3: HISTONE_H2B (D:1289-1311,H:1489-1511)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H2A
PS00046
Histone H2A signature.
H2A1_XENLA
22-28
2
C:821-827
G:1021-1027
2
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H32_XENLA
67-75
2
A:466-474
E:666-674
3
HISTONE_H2B
PS00357
Histone H2B signature.
H2B11_XENLA
93-115
2
D:1289-1311
H:1489-1511
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1s32c_ (C:)
1b: SCOP_d1s32g_ (G:)
2a: SCOP_d1s32d_ (D:)
2b: SCOP_d1s32h_ (H:)
3a: SCOP_d1s32a_ (A:)
3b: SCOP_d1s32e_ (E:)
4a: SCOP_d1s32b_ (B:)
4b: SCOP_d1s32f_ (F:)
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Histone-fold
(277)
Superfamily
:
Histone-fold
(277)
Family
:
Nucleosome core histones
(247)
Protein domain
:
Histone H2A
(45)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(34)
1a
d1s32c_
C:
1b
d1s32g_
G:
Protein domain
:
Histone H2B
(48)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(35)
2a
d1s32d_
D:
2b
d1s32h_
H:
Protein domain
:
Histone H3
(58)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(39)
3a
d1s32a_
A:
3b
d1s32e_
E:
Protein domain
:
Histone H4
(60)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(38)
4a
d1s32b_
B:
4b
d1s32f_
F:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1s32A00 (A:438-535)
1b: CATH_1s32E00 (E:637-735)
1c: CATH_1s32H00 (H:1425-1522)
1d: CATH_1s32D00 (D:1222-1322)
1e: CATH_1s32F00 (F:215-302)
1f: CATH_1s32C00 (C:812-918)
1g: CATH_1s32G00 (G:1013-1119)
1h: CATH_1s32B00 (B:22-102)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Histone, subunit A
(62)
Homologous Superfamily
:
Histone, subunit A
(62)
[unclassified]
(10)
1a
1s32A00
A:438-535
1b
1s32E00
E:637-735
1c
1s32H00
H:1425-1522
1d
1s32D00
D:1222-1322
1e
1s32F00
F:215-302
1f
1s32C00
C:812-918
1g
1s32G00
G:1013-1119
1h
1s32B00
B:22-102
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Histone_1s32G01 (G:1017-1090)
1b: PFAM_Histone_1s32G02 (G:1017-1090)
1c: PFAM_Histone_1s32H01 (H:1428-1498)
1d: PFAM_Histone_1s32H02 (H:1428-1498)
1e: PFAM_Histone_1s32E01 (E:657-731)
1f: PFAM_Histone_1s32E02 (E:657-731)
1g: PFAM_Histone_1s32F01 (F:224-293)
1h: PFAM_Histone_1s32F02 (F:224-293)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Histone
(49)
Family
:
Histone
(46)
Xenopus laevis (African clawed frog)
(32)
1a
Histone-1s32G01
G:1017-1090
1b
Histone-1s32G02
G:1017-1090
1c
Histone-1s32H01
H:1428-1498
1d
Histone-1s32H02
H:1428-1498
1e
Histone-1s32E01
E:657-731
1f
Histone-1s32E02
E:657-731
1g
Histone-1s32F01
F:224-293
1h
Histone-1s32F02
F:224-293
[
close Pfam info
]
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Asym.Unit (281 KB)
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