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Getting 'Exon' information from database.
4BZB
Asym. Unit
Info
Asym.Unit (689 KB)
Biol.Unit 1 (677 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE TETRAMERIC DGTP-BOUND SAMHD1 MUTANT CATALYTIC CORE
Authors
:
X. Ji, H. Yang, Y. Wu, J. Yan, J. Mehrens, M. Delucia, C. Hao, A. M. Gronenb J. Skowronski, J. Ahn, Y. Xiong
Date
:
25 Jul 13 (Deposition) - 23 Oct 13 (Release) - 20 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.83
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hydrolase, Hiv Restriction Factor, Dntpase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Ji, Y. Wu, J. Yan, J. Mehrens, H. Yang, M. Delucia, C. Hao, A. M. Gronenborn, J. Skowronski, J. Ahn, Y. Xiong
Mechanism Of Allosteric Activation Of Samhd1 By Dgtp
Nat. Struct. Mol. Biol. V. 20 1304 2013
[
close entry info
]
Hetero Components
(2, 20)
Info
All Hetero Components
1a: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTa)
1b: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTb)
1c: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTc)
1d: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTd)
1e: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTe)
1f: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTf)
1g: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTg)
1h: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTh)
1i: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTi)
1j: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTj)
1k: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTk)
1l: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGTl)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DGT
12
Ligand/Ion
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:149 , LEU A:150 , ARG A:164 , ARG A:206 , HIS A:210 , HIS A:215 , HIS A:233 , LYS A:312 , TYR A:315 , ASP A:319 , ARG A:366 , TYR A:374 , GLN A:375 , MG A:750 , HOH A:2030 , HOH A:2052 , HOH A:2053 , HOH A:2057 , HOH A:2061 , HOH A:2065 , HOH A:2087 , HOH A:2220 , HOH A:2221 , HOH A:2222 , HOH A:2223
BINDING SITE FOR RESIDUE DGT A 700
02
AC2
SOFTWARE
DGT A:700 , HOH A:2052 , HOH A:2053 , HOH A:2084 , HOH A:2222
BINDING SITE FOR RESIDUE MG A 750
03
AC3
SOFTWARE
VAL A:156 , PHE A:157 , ILE A:325 , ARG A:372 , HIS A:376 , LYS A:377 , MG A:850 , DGT A:900 , HOH A:2136 , HOH A:2139 , HOH A:2224 , HOH A:2225 , HOH A:2226 , ASP C:330 , ARG C:333 , PHE C:337 , ARG C:352 , LYS C:354 , ASN C:358 , LYS C:523 , VAL D:117 , ILE D:118 , ASN D:119
BINDING SITE FOR RESIDUE DGT A 800
04
AC4
SOFTWARE
DGT A:800 , DGT A:900 , HOH A:2226 , LYS D:116
BINDING SITE FOR RESIDUE MG A 850
05
AC5
SOFTWARE
TYR A:155 , VAL A:156 , VAL A:378 , ARG A:451 , LYS A:455 , DGT A:800 , MG A:850 , HOH A:2181 , HOH A:2182 , HOH A:2226 , HOH A:2227 , HOH A:2228 , LYS C:523 , LYS D:116 , VAL D:117 , ILE D:118 , ASP D:137 , GLN D:142 , ARG D:145 , PHE D:165
BINDING SITE FOR RESIDUE DGT A 900
06
AC6
SOFTWARE
GLN B:149 , LEU B:150 , ARG B:164 , ARG B:206 , HIS B:210 , HIS B:215 , HIS B:233 , LYS B:312 , TYR B:315 , ASP B:319 , ARG B:366 , TYR B:374 , GLN B:375 , MG B:750 , HOH B:2026 , HOH B:2032 , HOH B:2052 , HOH B:2053 , HOH B:2057 , HOH B:2058 , HOH B:2063 , HOH B:2074 , HOH B:2101 , HOH B:2160 , HOH B:2259 , HOH B:2260 , HOH B:2261 , HOH B:2262
BINDING SITE FOR RESIDUE DGT B 700
07
AC7
SOFTWARE
DGT B:700 , HOH B:2052 , HOH B:2053 , HOH B:2098 , HOH B:2261
BINDING SITE FOR RESIDUE MG B 750
08
AC8
SOFTWARE
VAL B:156 , PHE B:157 , ILE B:325 , ARG B:372 , HIS B:376 , LYS B:377 , MG B:850 , DGT B:900 , HOH B:2153 , HOH B:2157 , HOH B:2263 , HOH B:2264 , HOH B:2265 , HOH B:2267 , VAL C:117 , ASN C:119 , HIS C:125 , ASP D:330 , ARG D:333 , PHE D:337 , ARG D:352 , LYS D:354 , ASN D:358 , LYS D:523
BINDING SITE FOR RESIDUE DGT B 800
09
AC9
SOFTWARE
DGT B:800 , DGT B:900 , HOH B:2265
BINDING SITE FOR RESIDUE MG B 850
10
BC1
SOFTWARE
TYR B:155 , VAL B:156 , VAL B:378 , ARG B:451 , LYS B:455 , DGT B:800 , MG B:850 , HOH B:2199 , HOH B:2200 , HOH B:2265 , HOH B:2266 , HOH B:2268 , HOH B:2269 , HOH B:2270 , HOH B:2271 , LYS C:116 , VAL C:117 , ILE C:118 , ASP C:137 , GLN C:142 , ARG C:145 , PHE C:165 , LYS D:523
BINDING SITE FOR RESIDUE DGT B 900
11
BC2
SOFTWARE
GLN C:149 , LEU C:150 , ARG C:164 , ARG C:206 , HIS C:210 , HIS C:215 , HIS C:233 , ASP C:311 , LYS C:312 , TYR C:315 , ASP C:319 , ARG C:366 , TYR C:374 , GLN C:375 , MG C:750 , HOH C:2024 , HOH C:2045 , HOH C:2046 , HOH C:2050 , HOH C:2053 , HOH C:2068 , HOH C:2070 , HOH C:2152 , HOH C:2153
BINDING SITE FOR RESIDUE DGT C 700
12
BC3
SOFTWARE
DGT C:700 , HOH C:2045 , HOH C:2046 , HOH C:2068 , HOH C:2152
BINDING SITE FOR RESIDUE MG C 750
13
BC4
SOFTWARE
ASP A:330 , ARG A:333 , PHE A:337 , ARG A:352 , LYS A:354 , ASN A:358 , LYS A:523 , HOH A:2121 , HOH A:2123 , VAL B:117 , ASN B:119 , HOH B:2003 , VAL C:156 , PHE C:157 , ARG C:372 , HIS C:376 , LYS C:377 , MG C:850 , DGT C:900 , HOH C:2100 , HOH C:2103 , HOH C:2154 , HOH C:2155
BINDING SITE FOR RESIDUE DGT C 800
14
BC5
SOFTWARE
HOH B:2003 , DGT C:800 , DGT C:900
BINDING SITE FOR RESIDUE MG C 850
15
BC6
SOFTWARE
LYS A:523 , LYS B:116 , VAL B:117 , ILE B:118 , ASP B:137 , GLN B:142 , ARG B:145 , PHE B:165 , HOH B:2003 , HOH B:2004 , TYR C:155 , VAL C:156 , VAL C:378 , ARG C:451 , LYS C:455 , DGT C:800 , MG C:850 , HOH C:2125 , HOH C:2128 , HOH C:2129 , HOH C:2131 , HOH C:2156
BINDING SITE FOR RESIDUE DGT C 900
16
BC7
SOFTWARE
GLN D:149 , LEU D:150 , ARG D:164 , ARG D:206 , HIS D:210 , HIS D:215 , HIS D:233 , LYS D:312 , TYR D:315 , ASP D:319 , ARG D:366 , TYR D:374 , GLN D:375 , MG D:750 , HOH D:2022 , HOH D:2025 , HOH D:2026 , HOH D:2049 , HOH D:2050 , HOH D:2054 , HOH D:2055 , HOH D:2060 , HOH D:2064 , HOH D:2087 , HOH D:2090 , HOH D:2134 , HOH D:2214 , HOH D:2215 , HOH D:2217 , HOH D:2218
BINDING SITE FOR RESIDUE DGT D 700
17
BC8
SOFTWARE
DGT D:700 , HOH D:2049 , HOH D:2050 , HOH D:2087 , HOH D:2217
BINDING SITE FOR RESIDUE MG D 750
18
BC9
SOFTWARE
VAL A:117 , ILE A:118 , ASN A:119 , HOH A:2004 , ASP B:330 , ARG B:333 , PHE B:337 , ARG B:352 , LYS B:354 , ASN B:358 , LYS B:523 , HOH B:2135 , HOH B:2139 , VAL D:156 , PHE D:157 , ARG D:372 , HIS D:376 , LYS D:377 , MG D:850 , DGT D:900 , HOH D:2127 , HOH D:2132 , HOH D:2219 , HOH D:2220
BINDING SITE FOR RESIDUE DGT D 800
19
CC1
SOFTWARE
HOH A:2004 , DGT D:800 , DGT D:900
BINDING SITE FOR RESIDUE MG D 850
20
CC2
SOFTWARE
LYS A:116 , VAL A:117 , ILE A:118 , ASP A:137 , GLN A:142 , ARG A:145 , PHE A:165 , HOH A:2004 , HOH A:2005 , LYS B:523 , HOH B:2232 , TYR D:155 , VAL D:156 , VAL D:378 , ARG D:451 , LYS D:455 , DGT D:800 , MG D:850 , HOH D:2162 , HOH D:2163 , HOH D:2164 , HOH D:2221 , HOH D:2222
BINDING SITE FOR RESIDUE DGT D 900
[
close Site info
]
SAPs(SNPs)/Variants
(11, 44)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_058481 (H123P, chain A/B/C/D, )
02: VAR_058482 (R143C, chain A/B/C/D, )
03: VAR_058483 (R143H, chain A/B/C/D, )
04: VAR_058484 (R145Q, chain A/B/C/D, )
05: VAR_070633 (H167Y, chain A/B/C/D, )
06: VAR_058485 (I201N, chain A/B/C/D, )
07: VAR_058486 (G209S, chain A/B/C/D, )
08: VAR_058487 (M254V, chain A/B/C/D, )
09: VAR_070634 (R290H, chain A/B/C/D, )
10: VAR_058488 (L369S, chain A/B/C/D, )
11: VAR_058489 (M385V, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_058481
H
123
P
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
H
123
P
02
UniProt
VAR_058482
R
143
C
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
R
143
C
03
UniProt
VAR_058483
R
143
H
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
R
143
H
04
UniProt
VAR_058484
R
145
Q
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
R
145
Q
05
UniProt
VAR_070633
H
167
Y
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
H
167
Y
06
UniProt
VAR_058485
I
201
N
SAMH1_HUMAN
Disease (CHBL2)
---
A/B/C/D
I
201
N
07
UniProt
VAR_058486
G
209
S
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
G
209
S
08
UniProt
VAR_058487
M
254
V
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
M
254
V
09
UniProt
VAR_070634
R
290
H
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
R
290
H
10
UniProt
VAR_058488
L
369
S
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
L
369
S
11
UniProt
VAR_058489
M
385
V
SAMH1_HUMAN
Disease (AGS5)
---
A/B/C/D
M
385
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: HD (A:164-316,B:164-316,C:164-316,D:16...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HD
PS51831
HD domain profile.
SAMH1_HUMAN
164-316
4
A:164-316
B:164-316
C:164-316
D:164-316
[
close PROSITE info
]
Exons
(14, 56)
Info
All Exons
Exon 1.3 (A:113-116 | B:113-116 | C:113-116 ...)
Exon 1.4 (A:117-170 | B:117-170 | C:117-170 ...)
Exon 1.5 (A:170-209 | B:170-209 | C:170-209 ...)
Exon 1.6 (A:209-232 | B:209-232 | C:209-232 ...)
Exon 1.7 (A:233-284 (gaps) | B:233-284 (gaps...)
Exon 1.8 (A:285-318 | B:285-318 | C:285-318 ...)
Exon 1.9 (A:318-354 | B:318-354 | C:318-354 ...)
Exon 1.10 (A:355-385 | B:355-385 | C:355-385 ...)
Exon 1.11 (A:385-424 | B:385-424 | C:385-424 ...)
Exon 1.12a (A:424-470 | B:424-470 | C:424-470 ...)
Exon 1.13 (A:471-501 | B:471-501 | C:471-501 ...)
Exon 1.14 (A:502-536 | B:502-536 | C:502-536 ...)
Exon 1.15a (A:537-582 | B:537-582 | C:537-582 ...)
Exon 1.16 (A:583-599 | B:583-599 | C:583-599 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2/1.3
02: Boundary 1.3/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12a
11: Boundary 1.12a/1.13
12: Boundary 1.13/1.14
13: Boundary 1.14/1.15a
14: Boundary 1.15a/1.16
15: Boundary 1.16/-
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
ENST00000262878
1a
ENSE00001898623
chr20:
35580246-35579839
408
SAMH1_HUMAN
1-70
70
0
-
-
1.2
ENST00000262878
2
ENSE00001678776
chr20:
35575207-35575141
67
SAMH1_HUMAN
70-92
23
0
-
-
1.3
ENST00000262878
3
ENSE00001650543
chr20:
35569514-35569442
73
SAMH1_HUMAN
92-116
25
4
A:113-116
B:113-116
C:113-116
D:113-116
4
4
4
4
1.4
ENST00000262878
4
ENSE00001681376
chr20:
35563592-35563432
161
SAMH1_HUMAN
117-170
54
4
A:117-170
B:117-170
C:117-170
D:117-170
54
54
54
54
1.5
ENST00000262878
5
ENSE00001594973
chr20:
35559278-35559163
116
SAMH1_HUMAN
170-209
40
4
A:170-209
B:170-209
C:170-209
D:170-209
40
40
40
40
1.6
ENST00000262878
6
ENSE00001630356
chr20:
35555655-35555585
71
SAMH1_HUMAN
209-232
24
4
A:209-232
B:209-232
C:209-232
D:209-232
24
24
24
24
1.7
ENST00000262878
7
ENSE00001752622
chr20:
35547922-35547767
156
SAMH1_HUMAN
233-284
52
4
A:233-284 (gaps)
B:233-284 (gaps)
C:233-284 (gaps)
D:233-284 (gaps)
52
52
52
52
1.8
ENST00000262878
8
ENSE00001667406
chr20:
35545452-35545352
101
SAMH1_HUMAN
285-318
34
4
A:285-318
B:285-318
C:285-318
D:285-318
34
34
34
34
1.9
ENST00000262878
9
ENSE00001793017
chr20:
35545233-35545125
109
SAMH1_HUMAN
318-354
37
4
A:318-354
B:318-354
C:318-354
D:318-354
37
37
37
37
1.10
ENST00000262878
10
ENSE00001711142
chr20:
35540955-35540864
92
SAMH1_HUMAN
355-385
31
4
A:355-385
B:355-385
C:355-385
D:355-385
31
31
31
31
1.11
ENST00000262878
11
ENSE00001622813
chr20:
35539736-35539621
116
SAMH1_HUMAN
385-424
40
4
A:385-424
B:385-424
C:385-424
D:385-424
40
40
40
40
1.12a
ENST00000262878
12a
ENSE00000661815
chr20:
35533906-35533767
140
SAMH1_HUMAN
424-470
47
4
A:424-470
B:424-470
C:424-470
D:424-470
47
47
47
47
1.13
ENST00000262878
13
ENSE00000661814
chr20:
35532652-35532560
93
SAMH1_HUMAN
471-501
31
4
A:471-501
B:471-501
C:471-501
D:471-501
31
31
31
31
1.14
ENST00000262878
14
ENSE00000661813
chr20:
35526947-35526843
105
SAMH1_HUMAN
502-536
35
4
A:502-536
B:502-536
C:502-536
D:502-536
35
35
35
35
1.15a
ENST00000262878
15a
ENSE00000661812
chr20:
35526362-35526225
138
SAMH1_HUMAN
537-582
46
4
A:537-582
B:537-582
C:537-582
D:537-582
46
46
46
46
1.16
ENST00000262878
16
ENSE00000800455
chr20:
35521469-35518632
2838
SAMH1_HUMAN
583-626
44
4
A:583-599
B:583-599
C:583-599
D:583-599
17
17
17
17
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
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Choose
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background
color...
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RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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