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1TDH
Asym. Unit
Info
Asym.Unit (56 KB)
Biol.Unit 1 (52 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ENDONUCLEASE VIII-LIKE 1 (NEIL1)
Authors
:
S. Doublie, V. Bandaru, J. P. Bond, S. S. Wallace
Date
:
22 May 04 (Deposition) - 20 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Helix Two Turns Helix, Zinc-Less Finger, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Doublie, V. Bandaru, J. P. Bond, S. S. Wallace
The Crystal Structure Of Human Endonuclease Viii-Like 1 (Neil1) Reveals A Zincless Finger Motif Required For Glycosylase Activity.
Proc. Natl. Acad. Sci. Usa V. 101 10284 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:2 , LYS A:54 , ARG A:78 , GLY A:80 , HOH A:1015 , HOH A:1173 , HOH A:1188 , HOH A:1307 , HOH A:1310
BINDING SITE FOR RESIDUE TRS A 2000
[
close Site info
]
SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020580 (S82C, chain A, )
2: VAR_020581 (G83D, chain A, )
3: VAR_020582 (C136R, chain A, )
4: VAR_065963 (R159Q, chain A, )
5: VAR_065964 (E181K, chain A, )
6: VAR_020583 (I182M, chain A, )
7: VAR_065018 (R242R, chain A, )
8: VAR_020584 (D252N, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020580
S
82
C
NEIL1_HUMAN
Polymorphism
5745905
A
S
82
C
2
UniProt
VAR_020581
G
83
D
NEIL1_HUMAN
Polymorphism
5745906
A
G
83
D
3
UniProt
VAR_020582
C
136
R
NEIL1_HUMAN
Polymorphism
5745907
A
C
136
R
4
UniProt
VAR_065963
R
159
Q
NEIL1_HUMAN
Polymorphism
---
A
R
159
Q
5
UniProt
VAR_065964
E
181
K
NEIL1_HUMAN
Unclassified
---
A
E
181
K
6
UniProt
VAR_020583
I
182
M
NEIL1_HUMAN
Polymorphism
7183491
A
I
182
M
7
UniProt
VAR_065018
K
242
R
NEIL1_HUMAN
Unclassified
---
A
R
242
R
8
UniProt
VAR_020584
D
252
N
NEIL1_HUMAN
Polymorphism
5745926
A
D
252
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: FPG_CAT (A:2-121)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FPG_CAT
PS51068
Formamidopyrimidine-DNA glycosylase catalytic domain profile.
NEIL1_HUMAN
2-121
1
A:2-121
[
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]
Exons
(6, 6)
Info
All Exons
Exon 1.2a (A:2-145)
Exon 1.3 (A:145-185)
Exon 1.4 (A:185-202)
Exon 1.5 (A:208-240)
Exon 1.6 (A:240-282)
Exon 1.7 (A:283-290)
View:
Select:
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All Exon Boundaries
1: Boundary 1.1/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/1.8
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
1.1
ENST00000355059
1
ENSE00001520211
chr15:
75639331-75639814
484
NEIL1_HUMAN
-
0
0
-
-
1.2a
ENST00000355059
2a
ENSE00001433155
chr15:
75641225-75641680
456
NEIL1_HUMAN
1-145
145
1
A:2-145
144
1.3
ENST00000355059
3
ENSE00001616377
chr15:
75644452-75644571
120
NEIL1_HUMAN
145-185
41
1
A:145-185
41
1.4
ENST00000355059
4
ENSE00001616331
chr15:
75644665-75644728
64
NEIL1_HUMAN
185-206
22
1
A:185-202
18
1.5
ENST00000355059
5
ENSE00001768651
chr15:
75644943-75645042
100
NEIL1_HUMAN
207-240
34
1
A:208-240
33
1.6
ENST00000355059
6
ENSE00001622474
chr15:
75646080-75646207
128
NEIL1_HUMAN
240-282
43
1
A:240-282
43
1.7
ENST00000355059
7
ENSE00001625412
chr15:
75646591-75646618
28
NEIL1_HUMAN
283-292
10
1
A:283-290
8
1.8
ENST00000355059
8
ENSE00001603235
chr15:
75646772-75646833
62
NEIL1_HUMAN
292-312
21
0
-
-
1.9
ENST00000355059
9
ENSE00001737551
chr15:
75646994-75647159
166
NEIL1_HUMAN
313-368
56
0
-
-
1.10b
ENST00000355059
10b
ENSE00001806216
chr15:
75647305-75647592
288
NEIL1_HUMAN
368-390
23
0
-
-
[
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]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1tdha1 (A:132-246)
2a: SCOP_d1tdha2 (A:2-131)
3a: SCOP_d1tdha3 (A:247-290)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
S13-like H2TH domain
(119)
Superfamily
:
S13-like H2TH domain
(119)
Family
:
Middle domain of MutM-like DNA repair proteins
(41)
Protein domain
:
Endonuclease VIII-like 1 (NEIL1)
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1tdha1
A:132-246
Class
:
All beta proteins
(24004)
Fold
:
N-terminal domain of MutM-like DNA repair proteins
(42)
Superfamily
:
N-terminal domain of MutM-like DNA repair proteins
(42)
Family
:
N-terminal domain of MutM-like DNA repair proteins
(42)
Protein domain
:
Endonuclease VIII-like 1 (NEIL1)
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1tdha2
A:2-131
Class
:
Small proteins
(3458)
Fold
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Superfamily
:
Glucocorticoid receptor-like (DNA-binding domain)
(292)
Family
:
C-terminal, Zn-finger domain of MutM-like DNA repair proteins
(41)
Protein domain
:
Endonuclease VIII-like 1 (NEIL1)
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
3a
d1tdha3
A:247-290
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_H2TH_1tdhA01 (A:134-221)
2a: PFAM_Fapy_DNA_glyco_1tdhA02 (A:2-124)
3a: PFAM_Neil1_DNA_bind_1tdhA03 (A:252-290)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
H2TH
(43)
Family
:
H2TH
(20)
Homo sapiens (Human)
(1)
1a
H2TH-1tdhA01
A:134-221
Clan
:
no clan defined [family: Fapy_DNA_glyco]
(20)
Family
:
Fapy_DNA_glyco
(20)
Homo sapiens (Human)
(1)
2a
Fapy_DNA_glyco-1tdhA02
A:2-124
Clan
:
no clan defined [family: Neil1-DNA_bind]
(1)
Family
:
Neil1-DNA_bind
(1)
Homo sapiens (Human)
(1)
3a
Neil1-DNA_bind-1tdhA03
A:252-290
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Chain A
Asymmetric Unit 1
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