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1KQN
Asym. Unit
Info
Asym.Unit (251 KB)
Biol.Unit 1 (243 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NMN/NAMN ADENYLYLTRANSFERASE COMPLEXED WITH NAD
Authors
:
T. Zhou, O. Kurnasov, D. R. Tomchick, D. D. Binns, N. V. Grishin, V. E. Marquez, A. L. Osterman, H. Zhang
Date
:
07 Jan 02 (Deposition) - 07 Jan 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Nucleotidyltransferase Superfamily
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Zhou, O. Kurnasov, D. R. Tomchick, D. D. Binns, N. V. Grishin, V. E. Marquez, A. L. Osterman, H. Zhang
Structure Of Human Nicotinamide/Nicotonic Acid Mononucleotide Adenylyltransferase. Basis For The Dual Substrate Specificity And Activation Of The Oncolytic Agent Tiazofurin.
J. Biol. Chem. V. 277 13148 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 21)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2a: XENON (XEa)
2b: XENON (XEb)
2c: XENON (XEc)
2d: XENON (XEd)
2e: XENON (XEe)
2f: XENON (XEf)
2g: XENON (XEg)
2h: XENON (XEh)
2i: XENON (XEi)
2j: XENON (XEj)
2k: XENON (XEk)
2l: XENON (XEl)
2m: XENON (XEm)
2n: XENON (XEn)
2o: XENON (XEo)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
6
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
XE
15
Ligand/Ion
XENON
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:14 , GLY A:15 , SER A:16 , PHE A:17 , MET A:23 , HIS A:24 , LEU A:27 , TYR A:55 , LYS A:57 , TRP A:92 , GLU A:94 , THR A:95 , CYS A:155 , GLY A:156 , LEU A:159 , LEU A:168 , TRP A:169 , VAL A:186 , GLU A:215 , ASN A:219 , HOH A:779 , HOH A:781 , HOH A:785 , HOH A:795 , HOH A:798 , HOH A:813 , HOH A:857
BINDING SITE FOR RESIDUE NAD A 777
02
AC2
SOFTWARE
CYS B:14 , GLY B:15 , SER B:16 , PHE B:17 , MET B:23 , HIS B:24 , LEU B:27 , VAL B:51 , TYR B:55 , LYS B:57 , TRP B:92 , GLU B:94 , THR B:95 , CYS B:155 , GLY B:156 , ASP B:158 , LEU B:159 , LEU B:168 , TRP B:169 , VAL B:186 , GLU B:215 , ASN B:219 , HOH B:784 , HOH B:787 , HOH B:788 , HOH B:800 , HOH B:810 , HOH B:813
BINDING SITE FOR RESIDUE NAD B 778
03
AC3
SOFTWARE
CYS C:14 , GLY C:15 , SER C:16 , PHE C:17 , MET C:23 , HIS C:24 , LEU C:27 , VAL C:51 , TYR C:55 , LYS C:57 , TRP C:92 , GLU C:94 , THR C:95 , CYS C:155 , GLY C:156 , LEU C:159 , LEU C:168 , TRP C:169 , VAL C:186 , GLU C:215 , ASN C:219 , HOH C:781 , HOH C:782 , HOH C:790 , HOH C:795 , HOH C:809
BINDING SITE FOR RESIDUE NAD C 779
04
AC4
SOFTWARE
CYS D:14 , GLY D:15 , SER D:16 , PHE D:17 , MET D:23 , HIS D:24 , LEU D:27 , VAL D:51 , TYR D:55 , LYS D:57 , TRP D:92 , GLU D:94 , THR D:95 , CYS D:155 , GLY D:156 , LEU D:159 , LEU D:168 , TRP D:169 , VAL D:186 , GLU D:215 , ASN D:219 , HOH D:782 , HOH D:787 , HOH D:788 , HOH D:792 , HOH D:795 , HOH D:805 , HOH D:844
BINDING SITE FOR RESIDUE NAD D 780
05
AC5
SOFTWARE
CYS E:14 , GLY E:15 , SER E:16 , PHE E:17 , MET E:23 , HIS E:24 , LEU E:27 , TYR E:55 , LYS E:57 , TRP E:92 , GLU E:94 , THR E:95 , CYS E:155 , GLY E:156 , ASP E:158 , LEU E:159 , LEU E:168 , TRP E:169 , VAL E:186 , HOH E:789 , HOH E:790 , HOH E:798 , HOH E:799 , HOH E:806 , HOH E:815 , HOH E:820 , HOH E:844 , HOH E:861
BINDING SITE FOR RESIDUE NAD E 781
06
AC6
SOFTWARE
CYS F:14 , GLY F:15 , SER F:16 , PHE F:17 , MET F:23 , HIS F:24 , LEU F:27 , TYR F:55 , LYS F:57 , TRP F:92 , GLU F:94 , THR F:95 , CYS F:155 , GLY F:156 , LEU F:159 , LEU F:168 , TRP F:169 , VAL F:186 , GLU F:215 , ASN F:219 , HOH F:789 , HOH F:790 , HOH F:792 , HOH F:812 , HOH F:820 , HOH F:822 , HOH F:839
BINDING SITE FOR RESIDUE NAD F 782
07
AC7
SOFTWARE
LEU A:88
BINDING SITE FOR RESIDUE XE A 748
08
AC8
SOFTWARE
MET A:23 , LEU A:27 , GLU A:215 , ASN A:219
BINDING SITE FOR RESIDUE XE A 749
09
AC9
SOFTWARE
MET C:23 , LEU C:27 , GLU C:215
BINDING SITE FOR RESIDUE XE C 753
10
BC1
SOFTWARE
MET B:23 , GLU B:215
BINDING SITE FOR RESIDUE XE B 755
11
BC2
SOFTWARE
MET F:23 , LEU F:27
BINDING SITE FOR RESIDUE XE F 756
12
BC3
SOFTWARE
HIS E:24 , LEU E:27
BINDING SITE FOR RESIDUE XE E 757
13
BC4
SOFTWARE
LEU E:27
BINDING SITE FOR RESIDUE XE E 758
14
BC5
SOFTWARE
HIS B:24 , LEU B:27
BINDING SITE FOR RESIDUE XE B 760
15
BC6
SOFTWARE
HIS D:24 , LEU D:27
BINDING SITE FOR RESIDUE XE D 761
16
BC7
SOFTWARE
MET D:23 , LEU D:27 , GLU D:215
BINDING SITE FOR RESIDUE XE D 762
[
close Site info
]
SAPs(SNPs)/Variants
(28, 164)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_068856 (V9M, chain A/B/C/D/E/F, )
02: VAR_068857 (A13T, chain A/B/C/D/E/F, )
03: VAR_068858 (I20N, chain A/B/C/D/E/F, )
04: VAR_068859 (D33G, chain A/B/C/D/E/F, )
05: VAR_068860 (M35T, chain A/B/C/D/E/F, )
06: VAR_068861 (A54V, chain A/B/C/D/E/F, )
07: VAR_068862 (R66W, chain A/B/C/D/E/F, )
08: VAR_068863 (V67F, chain A/B/C/D/E/F, )
09: VAR_068864 (M69V, chain A/B/C/D/E/F, )
10: VAR_068865 (L72H, chain A/B/C/D/E/F, )
11: VAR_068866 (V98G, chain A/B/C/D/E/F, )
12: VAR_068867 (A147P, chain A/E, )
13: VAR_068868 (V151F, chain A/B/C/D/E/F, )
14: VAR_068869 (L153P, chain A/B/C/D/E/F, )
15: VAR_068870 (L153V, chain A/B/C/D/E/F, )
16: VAR_068871 (G156R, chain A/B/C/D/E/F, )
17: VAR_068872 (D173G, chain A/B/C/D/E/F, )
18: VAR_068873 (V178M, chain A/B/C/D/E/F, )
19: VAR_068874 (Y181C, chain A/B/C/D/E/F, )
20: VAR_068875 (I184M, chain A/B/C/D/E/F, )
21: VAR_068876 (R207W, chain A/B/C/D/E/F, )
22: VAR_068877 (I217N, chain A/B/C/D/E/F, )
23: VAR_068878 (R237C, chain A/B/C/D/E/F, )
24: VAR_068879 (R237L, chain A/B/C/D/E/F, )
25: VAR_068880 (L239S, chain A/B/C/D/E/F, )
26: VAR_068881 (H251P, chain A/B/C/D/E/F, )
27: VAR_068882 (E257K, chain A/B/C/D/E/F, )
28: VAR_068883 (N273D, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_068856
V
9
M
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
V
9
M
02
UniProt
VAR_068857
A
13
T
NMNA1_HUMAN
Disease (LCA9)
138613460
A/B/C/D/E/F
A
13
T
03
UniProt
VAR_068858
I
20
N
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
I
20
N
04
UniProt
VAR_068859
D
33
G
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
D
33
G
05
UniProt
VAR_068860
M
35
T
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
M
35
T
06
UniProt
VAR_068861
A
54
V
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
A
54
V
07
UniProt
VAR_068862
R
66
W
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
R
66
W
08
UniProt
VAR_068863
V
67
F
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
V
67
F
09
UniProt
VAR_068864
M
69
V
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
M
69
V
10
UniProt
VAR_068865
L
72
H
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
L
72
H
11
UniProt
VAR_068866
V
98
G
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
V
98
G
12
UniProt
VAR_068867
A
147
P
NMNA1_HUMAN
Disease (LCA9)
---
A/E
A
147
P
13
UniProt
VAR_068868
V
151
F
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
V
151
F
14
UniProt
VAR_068869
L
153
P
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
L
153
P
15
UniProt
VAR_068870
L
153
V
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
L
153
V
16
UniProt
VAR_068871
G
156
R
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
G
156
R
17
UniProt
VAR_068872
D
173
G
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
D
173
G
18
UniProt
VAR_068873
V
178
M
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
V
178
M
19
UniProt
VAR_068874
Y
181
C
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
Y
181
C
20
UniProt
VAR_068875
I
184
M
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
I
184
M
21
UniProt
VAR_068876
R
207
W
NMNA1_HUMAN
Disease (LCA9)
142968179
A/B/C/D/E/F
R
207
W
22
UniProt
VAR_068877
I
217
N
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
I
217
N
23
UniProt
VAR_068878
R
237
C
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
R
237
C
24
UniProt
VAR_068879
R
237
L
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
R
237
L
25
UniProt
VAR_068880
L
239
S
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
L
239
S
26
UniProt
VAR_068881
H
251
P
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
H
251
P
27
UniProt
VAR_068882
E
257
K
NMNA1_HUMAN
Disease (LCA9)
150726175
A/B/C/D/E/F
E
257
K
28
UniProt
VAR_068883
N
273
D
NMNA1_HUMAN
Disease (LCA9)
---
A/B/C/D/E/F
N
273
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(4, 24)
Info
All Exons
Exon 1.2a (A:6-39 | B:6-39 | C:6-39 | D:6-39 ...)
Exon 1.3 (A:39-100 | B:39-100 | C:39-100 | D...)
Exon 1.4a (A:100-147 (gaps) | B:100-108 | C:1...)
Exon 1.6b (A:147-275 | B:148-275 | C:148-275 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4a
4: Boundary 1.4a/1.6b
5: Boundary 1.6b/-
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
ENST00000377205
1a
ENSE00001473110
chr1:
10003486-10003573
88
NMNA1_HUMAN
-
0
0
-
-
1.2a
ENST00000377205
2a
ENSE00002202044
chr1:
10032076-10032246
171
NMNA1_HUMAN
1-39
39
6
A:6-39
B:6-39
C:6-39
D:6-39
E:6-39
F:6-39
34
34
34
34
34
34
1.3
ENST00000377205
3
ENSE00001682224
chr1:
10035650-10035833
184
NMNA1_HUMAN
39-100
62
6
A:39-100
B:39-100
C:39-100
D:39-100
E:39-100
F:39-100
62
62
62
62
62
62
1.4a
ENST00000377205
4a
ENSE00001180526
chr1:
10041089-10041228
140
NMNA1_HUMAN
100-147
48
6
A:100-147 (gaps)
B:100-108
C:100-108
D:100-108
E:100-147 (gaps)
F:100-108
48
9
9
9
48
9
1.6b
ENST00000377205
6b
ENSE00001473095
chr1:
10042359-10045556
3198
NMNA1_HUMAN
147-279
133
6
A:147-275
B:148-275
C:148-275
D:148-275
E:147-275
F:148-275
129
128
128
128
129
128
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1kqna_ (A:)
1b: SCOP_d1kqnb_ (B:)
1c: SCOP_d1kqnc_ (C:)
1d: SCOP_d1kqnd_ (D:)
1e: SCOP_d1kqne_ (E:)
1f: SCOP_d1kqnf_ (F:)
View:
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Nucleotidylyl transferase
(325)
Family
:
Adenylyltransferase
(56)
Protein domain
:
Nicotinamide mononucleotide (NMN) adenylyltransferase
(22)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1kqna_
A:
1b
d1kqnb_
B:
1c
d1kqnc_
C:
1d
d1kqnd_
D:
1e
d1kqne_
E:
1f
d1kqnf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1kqnB00 (B:6-275)
1b: CATH_1kqnC00 (C:6-275)
1c: CATH_1kqnD00 (D:6-275)
1d: CATH_1kqnF00 (F:6-275)
1e: CATH_1kqnA00 (A:6-275)
1f: CATH_1kqnE00 (E:6-275)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Human (Homo sapiens)
(27)
1a
1kqnB00
B:6-275
1b
1kqnC00
C:6-275
1c
1kqnD00
D:6-275
1d
1kqnF00
F:6-275
1e
1kqnA00
A:6-275
1f
1kqnE00
E:6-275
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_CTP_transf_2_1kqnF01 (F:12-229)
1b: PFAM_CTP_transf_2_1kqnF02 (F:12-229)
1c: PFAM_CTP_transf_2_1kqnF03 (F:12-229)
1d: PFAM_CTP_transf_2_1kqnF04 (F:12-229)
1e: PFAM_CTP_transf_2_1kqnF05 (F:12-229)
1f: PFAM_CTP_transf_2_1kqnF06 (F:12-229)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HUP
(230)
Family
:
CTP_transf_2
(36)
Homo sapiens (Human)
(9)
1a
CTP_transf_2-1kqnF01
F:12-229
1b
CTP_transf_2-1kqnF02
F:12-229
1c
CTP_transf_2-1kqnF03
F:12-229
1d
CTP_transf_2-1kqnF04
F:12-229
1e
CTP_transf_2-1kqnF05
F:12-229
1f
CTP_transf_2-1kqnF06
F:12-229
[
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
Chain E
Chain F
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
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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)
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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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Asym.Unit (251 KB)
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