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2QKK
Asym. Unit
Info
Asym.Unit (339 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (63 KB)
Biol.Unit 4 (62 KB)
Biol.Unit 5 (62 KB)
Biol.Unit 6 (38 KB)
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(1)
Title
:
HUMAN RNASE H CATALYTIC DOMAIN MUTANT D210N IN COMPLEX WITH 14-MER RNA/DNA HYBRID
Authors
:
M. Nowotny, S. A. Gaidamakov, R. Ghirlando, S. M. Cerritelli, R. J. Crouch, W. Yang
Date
:
11 Jul 07 (Deposition) - 13 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,R,S,T,U,W,X,Z
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Biol. Unit 5: R,S,T,U (1x)
Biol. Unit 6: W,X,Z (1x)
Keywords
:
Rnase H; Rna/Dna Hybrid, Hydrolase/Dna/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Nowotny, S. A. Gaidamakov, R. Ghirlando, S. M. Cerritelli, R. J. Crouch, W. Yang
Structure Of Human Rnase H1 Complexed With An Rna/Dna Hybrid: Insight Into Hiv Reverse Transcription
Mol. Cell V. 28 264 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 17)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
2a: CHLORIDE ION (CLa)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
4a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
14
Ligand/Ion
CALCIUM ION
2
CL
1
Ligand/Ion
CHLORIDE ION
3
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:145 , GLU A:186 , ASN A:210 , CA A:1002 , A C:5 , C C:6
BINDING SITE FOR RESIDUE CA A 1001
02
AC2
SOFTWARE
ASP A:145 , ASP A:274 , CA A:1001 , HOH A:2003 , HOH A:2007 , C C:6 , HOH C:15
BINDING SITE FOR RESIDUE CA A 1002
03
AC3
SOFTWARE
ASP B:145 , ASN B:210 , ASP B:274 , HOH B:2002 , HOH B:2003 , HOH B:2004
BINDING SITE FOR RESIDUE CA B 1009
04
AC4
SOFTWARE
TYR B:143 , TYR F:143 , PHE F:267
BINDING SITE FOR RESIDUE CL B 2001
05
AC5
SOFTWARE
ASP E:145 , ASP E:274 , C G:6
BINDING SITE FOR RESIDUE CA E 1003
06
AC6
SOFTWARE
ASP E:145 , GLU E:186 , ASN E:210 , A G:5 , C G:6
BINDING SITE FOR RESIDUE CA E 1004
07
AC7
SOFTWARE
ASP F:145 , ASN F:210 , ASP F:274
BINDING SITE FOR RESIDUE CA F 1013
08
AC8
SOFTWARE
ASP I:145 , ASP I:274 , C K:6 , HOH K:26
BINDING SITE FOR RESIDUE CA I 1006
09
AC9
SOFTWARE
ASP J:145 , ASN J:210 , ASP J:274
BINDING SITE FOR RESIDUE CA J 1008
10
BC1
SOFTWARE
HOH M:11 , HOH M:12 , ASP M:145 , ASP M:274 , CA M:1014 , C O:6 , HOH O:15
BINDING SITE FOR RESIDUE CA M 1010
11
BC2
SOFTWARE
ASP M:145 , GLU M:186 , ASN M:210 , CA M:1010 , A O:5 , C O:6
BINDING SITE FOR RESIDUE CA M 1014
12
BC3
SOFTWARE
ASP N:145 , ASN N:210 , ASP N:274
BINDING SITE FOR RESIDUE CA N 1005
13
BC4
SOFTWARE
ASP R:145 , GLY R:146 , ASP R:274 , C T:6
BINDING SITE FOR RESIDUE CA R 1011
14
BC5
SOFTWARE
ASP S:145 , ASN S:210 , ASP S:274
BINDING SITE FOR RESIDUE CA S 1007
15
BC6
SOFTWARE
ASP W:145 , ASN W:210 , ASP W:274
BINDING SITE FOR RESIDUE CA W 1012
16
BC7
SOFTWARE
GLY A:266 , GLU A:271 , ASP A:286 , DA D:17 , HOH D:2004
BINDING SITE FOR RESIDUE TRS D 2003
17
BC8
SOFTWARE
THR A:219 , ILE A:256 , GLN A:257 , TRP A:258 , ASN R:220 , GLN R:223
BINDING SITE FOR RESIDUE MES A 2002
[
close Site info
]
SAPs(SNPs)/Variants
(2, 22)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_074561 (V142I, chain A/B/E/F/I/J/M/N/R/S/W, )
2: VAR_074562 (A185V, chain A/B/E/F/I/J/M/N/R/S/W, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_074561
V
142
I
RNH1_HUMAN
Disease (PEOB2)
766294940
A/B/E/F/I/J/M/N/R/S/W
V
142
I
2
UniProt
VAR_074562
A
185
V
RNH1_HUMAN
Disease (PEOB2)
1057517675
A/B/E/F/I/J/M/N/R/S/W
A
185
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 10)
Info
All PROSITE Patterns/Profiles
1: RNASE_H (A:136-282,B:136-282,E:136-282,F:13...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RNASE_H
PS50879
RNase H domain profile.
RNH1_HUMAN
136-282
10
A:136-282
B:136-282
E:136-282
F:136-282
I:136-282
J:136-282
N:136-281
R:136-282
S:136-282
W:136-282
[
close PROSITE info
]
Exons
(6, 65)
Info
All Exons
Exon 1.4 (A:133-137 (gaps) | B:134-137 | E:1...)
Exon 1.5b (A:137-170 | B:137-170 | E:137-170 ...)
Exon 1.6 (A:170-188 | B:170-188 | E:170-188 ...)
Exon 1.7 (A:189-217 | B:189-217 | E:189-217 ...)
Exon 1.8 (A:217-258 | B:217-258 | E:217-258 ...)
Exon 1.9a (A:259-286 | B:259-284 | E:259-283 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.4
2: Boundary 1.4/1.5b
3: Boundary 1.5b/1.6
4: Boundary 1.6/1.7
5: Boundary 1.7/1.8
6: Boundary 1.8/1.9a
7: Boundary 1.9a/-
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
ENST00000315212
1a
ENSE00001253796
chr2:
3606206-3605723
484
RNH1_HUMAN
1-43
43
0
-
-
1.3
ENST00000315212
3
ENSE00001764472
chr2:
3604494-3604379
116
RNH1_HUMAN
43-82
40
0
-
-
1.4
ENST00000315212
4
ENSE00001613471
chr2:
3599898-3599734
165
RNH1_HUMAN
82-137
56
10
A:133-137 (gaps)
B:134-137
E:135-137
F:133-137 (gaps)
I:136-137
J:134-137
-
N:135-137
R:135-137
S:135-137
W:135-137
33
4
3
33
2
4
-
3
3
3
3
1.5b
ENST00000315212
5b
ENSE00001792991
chr2:
3598062-3597963
100
RNH1_HUMAN
137-170
34
11
A:137-170
B:137-170
E:137-170
F:137-170 (gaps)
I:137-170
J:137-170
M:138-170
N:137-170 (gaps)
R:137-170
S:137-170
W:137-170 (gaps)
34
34
34
34
34
34
33
34
34
34
34
1.6
ENST00000315212
6
ENSE00001703361
chr2:
3596702-3596648
55
RNH1_HUMAN
170-188
19
11
A:170-188
B:170-188
E:170-188
F:170-188
I:170-188
J:170-188
M:170-188
N:170-188
R:170-188
S:170-188
W:170-188
19
19
19
19
19
19
19
19
19
19
19
1.7
ENST00000315212
7
ENSE00001702047
chr2:
3596314-3596230
85
RNH1_HUMAN
189-217
29
11
A:189-217
B:189-217
E:189-217
F:189-217
I:189-217
J:189-217
M:189-217
N:189-217
R:189-217
S:189-217
W:189-217
29
29
29
29
29
29
29
29
29
29
29
1.8
ENST00000315212
8
ENSE00001759845
chr2:
3595645-3595521
125
RNH1_HUMAN
217-258
42
11
A:217-258
B:217-258
E:217-258
F:217-258
I:217-258
J:217-258
M:217-258
N:217-258
R:217-258
S:217-258
W:217-258
42
42
42
42
42
42
42
42
42
42
42
1.9a
ENST00000315212
9a
ENSE00001253775
chr2:
3593461-3592705
757
RNH1_HUMAN
259-286
28
11
A:259-286
B:259-284
E:259-283
F:259-285
I:259-284
J:259-284
M:259-282
N:259-281
R:259-282
S:259-282
W:259-285
28
26
25
27
26
26
24
23
24
24
27
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 11)
Info
all PFAM domains
1a: PFAM_RNase_H_2qkkW01 (W:137-282)
1b: PFAM_RNase_H_2qkkW02 (W:137-282)
1c: PFAM_RNase_H_2qkkW03 (W:137-282)
1d: PFAM_RNase_H_2qkkW04 (W:137-282)
1e: PFAM_RNase_H_2qkkW05 (W:137-282)
1f: PFAM_RNase_H_2qkkW06 (W:137-282)
1g: PFAM_RNase_H_2qkkW07 (W:137-282)
1h: PFAM_RNase_H_2qkkW08 (W:137-282)
1i: PFAM_RNase_H_2qkkW09 (W:137-282)
1j: PFAM_RNase_H_2qkkW10 (W:137-282)
1k: PFAM_RNase_H_2qkkW11 (W:137-282)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
RNase_H
(288)
Family
:
RNase_H
(128)
Homo sapiens (Human)
(3)
1a
RNase_H-2qkkW01
W:137-282
1b
RNase_H-2qkkW02
W:137-282
1c
RNase_H-2qkkW03
W:137-282
1d
RNase_H-2qkkW04
W:137-282
1e
RNase_H-2qkkW05
W:137-282
1f
RNase_H-2qkkW06
W:137-282
1g
RNase_H-2qkkW07
W:137-282
1h
RNase_H-2qkkW08
W:137-282
1i
RNase_H-2qkkW09
W:137-282
1j
RNase_H-2qkkW10
W:137-282
1k
RNase_H-2qkkW11
W:137-282
[
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]
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Asym.Unit (339 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (64 KB)
Header - Biol.Unit 2
Biol.Unit 3 (63 KB)
Header - Biol.Unit 3
Biol.Unit 4 (62 KB)
Header - Biol.Unit 4
Biol.Unit 5 (62 KB)
Header - Biol.Unit 5
Biol.Unit 6 (38 KB)
Header - Biol.Unit 6
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