PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1P7L
Asym. Unit
Info
Asym.Unit (247 KB)
Biol.Unit 1 (240 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
S-ADENOSYLMETHIONINE SYNTHETASE COMPLEXED WITH AMPPNP AND MET.
Authors
:
F. Takusagawa, J. Komoto
Date
:
02 May 03 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
S-Adenosylmethionine Synthetase, Amppnp, Sam, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Komoto, T. Yamada, Y. Takata, G. D. Markham, F. Takusagawa
Crystal Structure Of The S-Adenosylmethionine Synthetase Ternary Complex: A Novel Catalytic Mechanism Of S-Adenosylmethionine Synthesis From Atp And Met.
Biochemistry V. 43 1821 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 20)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
3a: METHIONINE (METa)
3b: METHIONINE (METb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
5a: (DIPHOSPHONO)AMINOPHOSPHONIC ACID (PPKa)
5b: (DIPHOSPHONO)AMINOPHOSPHONIC ACID (PPKb)
6a: S-ADENOSYLMETHIONINE (SAMa)
6b: S-ADENOSYLMETHIONINE (SAMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
K
4
Ligand/Ion
POTASSIUM ION
3
MET
2
Mod. Amino Acid
METHIONINE
4
MG
8
Ligand/Ion
MAGNESIUM ION
5
PPK
2
Ligand/Ion
(DIPHOSPHONO)AMINOPHOSPHONIC ACID
6
SAM
2
Ligand/Ion
S-ADENOSYLMETHIONINE
[
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
ASP A:238 , CYS A:239 , ANP A:384 , GLU B:42
BINDING SITE FOR RESIDUE K A 386
02
AC2
SOFTWARE
LYS A:245 , ANP A:384
BINDING SITE FOR RESIDUE MG A 387
03
AC3
SOFTWARE
ASP A:16 , ANP A:384
BINDING SITE FOR RESIDUE MG A 388
04
AC4
SOFTWARE
GLU A:42 , ASP B:238 , CYS B:239 , ANP B:484
BINDING SITE FOR RESIDUE K B 486
05
AC5
SOFTWARE
LYS B:245 , ANP B:484
BINDING SITE FOR RESIDUE MG B 487
06
AC6
SOFTWARE
ASP B:16 , ANP B:484
BINDING SITE FOR RESIDUE MG B 488
07
AC7
SOFTWARE
ASP C:238 , CYS C:239 , PPK C:684 , GLU D:42
BINDING SITE FOR RESIDUE K C 686
08
AC8
SOFTWARE
PPK C:684 , ASP D:118 , ASP D:271
BINDING SITE FOR RESIDUE MG D 687
09
AC9
SOFTWARE
ASP C:16 , PPK C:684
BINDING SITE FOR RESIDUE MG C 688
10
BC1
SOFTWARE
GLU C:42 , ASP D:238 , CYS D:239 , PPK D:884
BINDING SITE FOR RESIDUE K D 886
11
BC2
SOFTWARE
ASP C:271 , PPK D:884
BINDING SITE FOR RESIDUE MG C 887
12
BC3
SOFTWARE
ASP D:16 , PPK D:884
BINDING SITE FOR RESIDUE MG D 888
13
BC4
SOFTWARE
HIS C:14 , PRO C:15 , ASP C:163 , LYS C:165 , THR C:227 , ARG C:229 , PHE C:230 , ASP C:238 , PPK C:684 , HOH C:700 , HOH C:702 , HOH C:711 , HOH C:716 , ALA D:40 , GLU D:55 , GLN D:98 , ASP D:101 , ILE D:102 , GLY D:117 , ASP D:118 , LYS D:269 , ILE D:302
BINDING SITE FOR RESIDUE SAM C 685
14
BC5
SOFTWARE
ALA C:40 , GLU C:55 , GLN C:98 , ASP C:101 , ILE C:102 , GLY C:117 , ASP C:118 , LYS C:269 , ILE C:302 , HOH C:900 , HOH C:902 , HIS D:14 , PRO D:15 , ASP D:163 , LYS D:165 , THR D:227 , ARG D:229 , PHE D:230 , ASP D:238 , PPK D:884 , HOH D:916
BINDING SITE FOR RESIDUE SAM C 885
15
BC6
SOFTWARE
HIS A:14 , PRO A:15 , ASP A:16 , ASP A:163 , LYS A:165 , SER A:186 , ARG A:229 , PHE A:230 , ASP A:238 , ARG A:244 , LYS A:245 , K A:386 , MG A:387 , MG A:388 , HOH A:411 , HOH A:413 , ILE B:102 , ASP B:118 , GLY B:259 , GLY B:260 , ALA B:261 , LYS B:265 , ASP B:271 , MET B:385
BINDING SITE FOR RESIDUE ANP A 384
16
BC7
SOFTWARE
ASP A:238 , ANP A:384 , HOH A:401 , ALA B:40 , GLU B:55 , GLN B:98 , ILE B:102 , GLY B:117 , ASP B:118 , LYS B:269 , ILE B:302 , HOH B:400
BINDING SITE FOR RESIDUE MET B 385
17
BC8
SOFTWARE
ASP A:101 , ILE A:102 , ASP A:118 , GLY A:259 , GLY A:260 , ALA A:261 , LYS A:265 , ASP A:271 , MET A:485 , HOH A:530 , HIS B:14 , PRO B:15 , ASP B:16 , ASP B:163 , LYS B:165 , SER B:186 , ARG B:229 , PHE B:230 , ASP B:238 , ARG B:244 , LYS B:245 , K B:486 , MG B:487 , MG B:488 , HOH B:513
BINDING SITE FOR RESIDUE ANP B 484
18
BC9
SOFTWARE
ALA A:40 , GLU A:55 , GLN A:98 , ILE A:102 , GLY A:117 , ASP A:118 , LYS A:269 , ILE A:302 , HOH A:500 , HOH A:501 , ASP B:238 , ANP B:484
BINDING SITE FOR RESIDUE MET A 485
19
CC1
SOFTWARE
HIS C:14 , ASP C:16 , LYS C:165 , ARG C:244 , LYS C:245 , SAM C:685 , K C:686 , MG C:688 , ASP D:118 , GLY D:259 , GLY D:260 , ALA D:261 , LYS D:265 , ASP D:271 , MG D:687
BINDING SITE FOR RESIDUE PPK C 684
20
CC2
SOFTWARE
ASP C:118 , GLY C:259 , GLY C:260 , ALA C:261 , LYS C:265 , ASP C:271 , SAM C:885 , MG C:887 , HOH C:930 , HIS D:14 , ASP D:16 , LYS D:165 , ARG D:244 , LYS D:245 , K D:886 , MG D:888
BINDING SITE FOR RESIDUE PPK D 884
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ADOMET_SYNTHASE_1 (A:115-125,B:115-125,C:115-125,D:11...)
2: ADOMET_SYNTHASE_2 (A:258-266,B:258-266,C:258-266,D:25...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADOMET_SYNTHASE_1
PS00376
S-adenosylmethionine synthase signature 1.
METK_ECOLI
116-126
4
A:115-125
B:115-125
C:115-125
D:115-125
2
ADOMET_SYNTHASE_2
PS00377
S-adenosylmethionine synthase signature 2.
METK_ECOLI
259-267
4
A:258-266
B:258-266
C:258-266
D:258-266
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1p7la1 (A:1-102)
1b: SCOP_d1p7la2 (A:103-231)
1c: SCOP_d1p7la3 (A:232-383)
1d: SCOP_d1p7lb1 (B:1-102)
1e: SCOP_d1p7lb2 (B:103-231)
1f: SCOP_d1p7lb3 (B:232-383)
1g: SCOP_d1p7lc1 (C:1-102)
1h: SCOP_d1p7lc2 (C:103-231)
1i: SCOP_d1p7lc3 (C:232-383)
1j: SCOP_d1p7ld1 (D:1-102)
1k: SCOP_d1p7ld2 (D:103-231)
1l: SCOP_d1p7ld3 (D:232-383)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
S-adenosylmethionine synthetase
(23)
Superfamily
:
S-adenosylmethionine synthetase
(23)
Family
:
S-adenosylmethionine synthetase
(15)
Protein domain
:
S-adenosylmethionine synthetase
(15)
Escherichia coli [TaxId: 562]
(9)
1a
d1p7la1
A:1-102
1b
d1p7la2
A:103-231
1c
d1p7la3
A:232-383
1d
d1p7lb1
B:1-102
1e
d1p7lb2
B:103-231
1f
d1p7lb3
B:232-383
1g
d1p7lc1
C:1-102
1h
d1p7lc2
C:103-231
1i
d1p7lc3
C:232-383
1j
d1p7ld1
D:1-102
1k
d1p7ld2
D:103-231
1l
d1p7ld3
D:232-383
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1p7lA03 (A:1-9,A:136-232)
1b: CATH_1p7lB03 (B:1-9,B:136-232)
1c: CATH_1p7lC02 (C:10-101,C:233-269)
1d: CATH_1p7lD02 (D:10-101,D:233-269)
1e: CATH_1p7lA01 (A:108-135,A:270-382)
1f: CATH_1p7lB01 (B:108-135,B:270-382)
1g: CATH_1p7lC01 (C:108-135,C:270-382)
1h: CATH_1p7lD01 (D:108-135,D:270-382)
1i: CATH_1p7lC03 (C:1-9,C:136-232)
1j: CATH_1p7lD03 (D:1-9,D:136-232)
1k: CATH_1p7lA02 (A:10-101,A:233-269)
1l: CATH_1p7lB02 (B:10-101,B:233-269)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GMP Synthetase; Chain A, domain 3
(192)
Homologous Superfamily
:
[code=3.30.300.10, no name defined]
(22)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1p7lA03
A:1-9,A:136-232
1b
1p7lB03
B:1-9,B:136-232
1c
1p7lC02
C:10-101,C:233-269
1d
1p7lD02
D:10-101,D:233-269
1e
1p7lA01
A:108-135,A:270-382
1f
1p7lB01
B:108-135,B:270-382
1g
1p7lC01
C:108-135,C:270-382
1h
1p7lD01
D:108-135,D:270-382
1i
1p7lC03
C:1-9,C:136-232
1j
1p7lD03
D:1-9,D:136-232
1k
1p7lA02
A:10-101,A:233-269
1l
1p7lB02
B:10-101,B:233-269
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_S_AdoMet_synt_C_1p7lD01 (D:232-369)
1b: PFAM_S_AdoMet_synt_C_1p7lD02 (D:232-369)
1c: PFAM_S_AdoMet_synt_C_1p7lD03 (D:232-369)
1d: PFAM_S_AdoMet_synt_C_1p7lD04 (D:232-369)
2a: PFAM_S_AdoMet_synt_M_1p7lD05 (D:112-230)
2b: PFAM_S_AdoMet_synt_M_1p7lD06 (D:112-230)
2c: PFAM_S_AdoMet_synt_M_1p7lD07 (D:112-230)
2d: PFAM_S_AdoMet_synt_M_1p7lD08 (D:112-230)
3a: PFAM_S_AdoMet_synt_N_1p7lD09 (D:1-100)
3b: PFAM_S_AdoMet_synt_N_1p7lD10 (D:1-100)
3c: PFAM_S_AdoMet_synt_N_1p7lD11 (D:1-100)
3d: PFAM_S_AdoMet_synt_N_1p7lD12 (D:1-100)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: S-AdoMet_synt_C]
(16)
Family
:
S-AdoMet_synt_C
(16)
Escherichia coli (strain K12)
(7)
1a
S-AdoMet_synt_C-1p7lD01
D:232-369
1b
S-AdoMet_synt_C-1p7lD02
D:232-369
1c
S-AdoMet_synt_C-1p7lD03
D:232-369
1d
S-AdoMet_synt_C-1p7lD04
D:232-369
Clan
:
no clan defined [family: S-AdoMet_synt_M]
(16)
Family
:
S-AdoMet_synt_M
(16)
Escherichia coli (strain K12)
(7)
2a
S-AdoMet_synt_M-1p7lD05
D:112-230
2b
S-AdoMet_synt_M-1p7lD06
D:112-230
2c
S-AdoMet_synt_M-1p7lD07
D:112-230
2d
S-AdoMet_synt_M-1p7lD08
D:112-230
Clan
:
no clan defined [family: S-AdoMet_synt_N]
(16)
Family
:
S-AdoMet_synt_N
(16)
Escherichia coli (strain K12)
(7)
3a
S-AdoMet_synt_N-1p7lD09
D:1-100
3b
S-AdoMet_synt_N-1p7lD10
D:1-100
3c
S-AdoMet_synt_N-1p7lD11
D:1-100
3d
S-AdoMet_synt_N-1p7lD12
D:1-100
[
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
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (247 KB)
Header - Asym.Unit
Biol.Unit 1 (240 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1P7L
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
