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2H94
Asym. Unit
Info
Asym.Unit (112 KB)
Biol.Unit 1 (106 KB)
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(1)
Title
:
CRYSTAL STRUCTURE AND MECHANISM OF HUMAN LYSINE-SPECIFIC DEMETHYLASE-1
Authors
:
P. Stavropoulos, G. Blobel, A. Hoelz
Date
:
08 Jun 06 (Deposition) - 04 Jul 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Histone Demethylase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Stavropoulos, G. Blobel, A. Hoelz
Crystal Structure And Mechanism Of Human Lysine-Specific Demethylase-1.
Nat. Struct. Mol. Biol. V. 13 626 2006
(for further references see the
PDB file header
)
[
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]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: MERCURY (II) ION (HGa)
2b: MERCURY (II) ION (HGb)
2c: MERCURY (II) ION (HGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
HG
3
Ligand/Ion
MERCURY (II) ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:360 , LEU A:362 , TRP A:531
BINDING SITE FOR RESIDUE HG A 1
2
AC2
SOFTWARE
GLN A:419
BINDING SITE FOR RESIDUE HG A 2
3
AC3
SOFTWARE
CYS A:573
BINDING SITE FOR RESIDUE HG A 3
4
AC4
SOFTWARE
GLY A:285 , GLY A:287 , VAL A:288 , SER A:289 , LEU A:307 , GLU A:308 , ALA A:309 , ARG A:310 , GLY A:315 , ARG A:316 , LEU A:329 , GLY A:330 , ALA A:331 , MET A:332 , VAL A:333 , VAL A:590 , THR A:624 , LEU A:625 , LEU A:659 , TRP A:756 , SER A:760 , TYR A:761 , GLY A:800 , GLU A:801 , THR A:810 , VAL A:811 , ALA A:814 , HOH A:5002 , HOH A:5005 , HOH A:5011
BINDING SITE FOR RESIDUE FAD A 5000
[
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]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_076366 (E379K, chain A, )
2: VAR_076367 (D556G, chain A, )
3: VAR_076368 (Y761H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_076366
E
379
K
KDM1A_HUMAN
Disease (CPRF)
864309715
A
E
379
K
2
UniProt
VAR_076367
D
556
G
KDM1A_HUMAN
Disease (CPRF)
864309716
A
D
556
G
3
UniProt
VAR_076368
Y
761
H
KDM1A_HUMAN
Disease (CPRF)
864309714
A
Y
761
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SWIRM (A:174-273)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SWIRM
PS50934
SWIRM domain profile.
KDM1A_HUMAN
174-273
1
A:174-273
[
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]
Exons
(18, 18)
Info
All Exons
Exon 1.2 (A:172-173)
Exon 1.4a (A:173-217)
Exon 1.5 (A:218-244)
Exon 1.6a (A:244-275)
Exon 1.7 (A:275-310)
Exon 1.8 (A:311-338)
Exon 1.9 (A:338-369)
Exon 1.11 (A:370-417)
Exon 1.12 (A:417-447)
Exon 1.13 (A:448-492 (gaps))
Exon 1.14 (A:493-517)
Exon 1.15b (A:517-554)
Exon 1.16a (A:555-599)
Exon 1.17b (A:599-661)
Exon 1.18b (A:662-700)
Exon 1.19 (A:700-742)
Exon 1.20 (A:743-783)
Exon 1.21c (A:793-835)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.4a
03: Boundary 1.4a/1.5
04: Boundary 1.5/1.6a
05: Boundary 1.6a/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/1.13
11: Boundary 1.13/1.14
12: Boundary 1.14/1.15b
13: Boundary 1.15b/1.16a
14: Boundary 1.16a/1.17b
15: Boundary 1.17b/1.18b
16: Boundary 1.18b/1.19
17: Boundary 1.19/1.20
18: Boundary 1.20/1.21c
19: Boundary 1.21c/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000356634
1a
ENSE00001422377
chr1:
23345941-23346440
500
KDM1A_HUMAN
1-117
117
0
-
-
1.2
ENST00000356634
2
ENSE00000388542
chr1:
23356962-23357127
166
KDM1A_HUMAN
118-173
56
1
A:172-173
2
1.4a
ENST00000356634
4a
ENSE00000759117
chr1:
23376880-23377013
134
KDM1A_HUMAN
173-217
45
1
A:173-217
45
1.5
ENST00000356634
5
ENSE00000859702
chr1:
23380254-23380332
79
KDM1A_HUMAN
218-244
27
1
A:218-244
27
1.6a
ENST00000356634
6a
ENSE00000859703
chr1:
23381562-23381654
93
KDM1A_HUMAN
244-275
32
1
A:244-275
32
1.7
ENST00000356634
7
ENSE00000859704
chr1:
23382425-23382531
107
KDM1A_HUMAN
275-310
36
1
A:275-310
36
1.8
ENST00000356634
8
ENSE00000859705
chr1:
23383977-23384058
82
KDM1A_HUMAN
311-338
28
1
A:311-338
28
1.9
ENST00000356634
9
ENSE00000759111
chr1:
23385566-23385660
95
KDM1A_HUMAN
338-369
32
1
A:338-369
32
1.11
ENST00000356634
11
ENSE00000759110
chr1:
23395032-23395174
143
KDM1A_HUMAN
370-417
48
1
A:370-417
48
1.12
ENST00000356634
12
ENSE00000759108
chr1:
23395554-23395644
91
KDM1A_HUMAN
417-447
31
1
A:417-447
31
1.13
ENST00000356634
13
ENSE00000859709
chr1:
23397718-23397852
135
KDM1A_HUMAN
448-492
45
1
A:448-492 (gaps)
45
1.14
ENST00000356634
14
ENSE00000759106
chr1:
23398617-23398690
74
KDM1A_HUMAN
493-517
25
1
A:493-517
25
1.15b
ENST00000356634
15b
ENSE00000388553
chr1:
23399785-23399896
112
KDM1A_HUMAN
517-554
38
1
A:517-554
38
1.16a
ENST00000356634
16a
ENSE00000759050
chr1:
23403721-23403853
133
KDM1A_HUMAN
555-599
45
1
A:555-599
45
1.17b
ENST00000356634
17b
ENSE00000859713
chr1:
23405483-23405670
188
KDM1A_HUMAN
599-661
63
1
A:599-661
63
1.18b
ENST00000356634
18b
ENSE00000859714
chr1:
23406046-23406160
115
KDM1A_HUMAN
662-700
39
1
A:662-700
39
1.19
ENST00000356634
19
ENSE00000859715
chr1:
23407939-23408066
128
KDM1A_HUMAN
700-742
43
1
A:700-742
43
1.20
ENST00000356634
20
ENSE00000759046
chr1:
23408713-23408859
147
KDM1A_HUMAN
743-791
49
1
A:743-783
41
1.21c
ENST00000356634
21c
ENSE00001564450
chr1:
23409672-23410182
511
KDM1A_HUMAN
792-852
61
1
A:793-835
43
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2h94a1 (A:172-273)
2a: SCOP_d2h94a3 (A:655-763)
3a: SCOP_d2h94a2 (A:274-654,A:764-835)
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Folds
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Superfamilies
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Families
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Homeodomain-like
(373)
Family
:
SWIRM domain
(14)
Protein domain
:
Lysine-specific histone demethylase 1, LSD1
(9)
Human (Homo sapiens) [TaxId: 9606]
(9)
1a
d2h94a1
A:172-273
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FAD-linked reductases, C-terminal domain
(181)
Superfamily
:
FAD-linked reductases, C-terminal domain
(181)
Family
:
L-aminoacid/polyamine oxidase
(66)
Protein domain
:
Lysine-specific histone demethylase 1, LSD1
(8)
Human (Homo sapiens) [TaxId: 9606]
(8)
2a
d2h94a3
A:655-763
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD-linked reductases, N-terminal domain
(156)
Protein domain
:
Lysine-specific histone demethylase 1, LSD1
(8)
Human (Homo sapiens) [TaxId: 9606]
(8)
3a
d2h94a2
A:274-654,A:764-835
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2h94A01 (A:172-279)
2a: CATH_2h94A03 (A:406-521)
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(
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
Human (Homo sapiens)
(70)
1a
2h94A01
A:172-279
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.80, no name defined]
(43)
Human (Homo sapiens)
(13)
2a
2h94A03
A:406-521
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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