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.
2NV1
Asym. Unit
Info
Asym.Unit (288 KB)
Biol.Unit 1 (549 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE SYNTHASE SUBUNIT PDX1 (YAAD) OF PLP SYNTHASE FROM BACILLUS SUBTILIS
Authors
:
M. Strohmeier, I. Tews, I. Sinning
Date
:
10 Nov 06 (Deposition) - 05 Dec 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.08
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
(Beta/Alpha)8-Barrel, Synthase, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Strohmeier, T. Raschle, J. Mazurkiewicz, K. Rippe, I. Sinning, T. B. Fitzpatrick, I. Tews
Structure Of A Bacterial Pyridoxal 5'-Phosphate Synthase Complex
Proc. Natl. Acad. Sci. Usa V. 103 19284 2006
[
close entry info
]
Hetero Components
(3, 35)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
12
Ligand/Ion
CHLORIDE ION
2
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
3
MG
12
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:137 , ARG A:138 , HOH A:4103 , HOH A:4214 , HOH A:4328
BINDING SITE FOR RESIDUE CL A 3001
02
AC2
SOFTWARE
GLY A:214 , HOH A:4186
BINDING SITE FOR RESIDUE CL A 3002
03
AC3
SOFTWARE
HOH A:4001 , HOH A:4002 , HOH A:4003 , HOH A:4004 , HOH F:4004 , HOH F:4005
BINDING SITE FOR RESIDUE MG A 3003
04
AC4
SOFTWARE
HOH A:4005 , HOH A:4006 , HOH A:4007 , HOH A:4008 , HOH A:4009 , HOH A:4010
BINDING SITE FOR RESIDUE MG A 3004
05
AC5
SOFTWARE
ARG B:137 , ARG B:138 , HOH B:4100 , HOH B:4327
BINDING SITE FOR RESIDUE CL B 3007
06
AC6
SOFTWARE
GLY B:153 , GLY B:214 , HOH B:4177
BINDING SITE FOR RESIDUE CL B 3008
07
AC7
SOFTWARE
HOH A:4011 , HOH A:4012 , HOH A:4013 , HOH B:4014 , HOH B:4015 , HOH B:4016
BINDING SITE FOR RESIDUE MG A 3009
08
AC8
SOFTWARE
HOH B:4017 , HOH B:4018 , HOH B:4019 , HOH B:4020 , HOH B:4021 , HOH B:4022
BINDING SITE FOR RESIDUE MG B 3010
09
AC9
SOFTWARE
ARG C:137 , ARG C:138 , HOH C:4107 , HOH C:4312
BINDING SITE FOR RESIDUE CL C 3013
10
BC1
SOFTWARE
GLY C:214
BINDING SITE FOR RESIDUE CL C 3014
11
BC2
SOFTWARE
HOH B:4023 , HOH B:4024 , HOH C:4026 , HOH C:4027 , HOH C:4028 , HOH C:4029
BINDING SITE FOR RESIDUE MG C 3015
12
BC3
SOFTWARE
HOH C:4030 , HOH C:4031 , HOH C:4032 , HOH C:4033 , HOH C:4034 , HOH C:4035
BINDING SITE FOR RESIDUE MG C 3016
13
BC4
SOFTWARE
ARG D:137 , ARG D:138 , HOH D:4113 , HOH D:4411
BINDING SITE FOR RESIDUE CL D 3020
14
BC5
SOFTWARE
GLY D:153 , GLY D:214 , HOH D:4128 , HOH D:4171
BINDING SITE FOR RESIDUE CL D 3021
15
BC6
SOFTWARE
HOH C:4036 , HOH C:4037 , HOH C:4038 , HOH D:4038 , HOH D:4039 , HOH D:4040
BINDING SITE FOR RESIDUE MG C 3022
16
BC7
SOFTWARE
HOH D:4041 , HOH D:4042 , HOH D:4043 , HOH D:4044 , HOH D:4045 , HOH D:4046
BINDING SITE FOR RESIDUE MG D 3023
17
BC8
SOFTWARE
ARG E:137 , ARG E:138 , HOH E:4141
BINDING SITE FOR RESIDUE CL E 3025
18
BC9
SOFTWARE
GLY E:153 , GLY E:214 , HOH E:4190 , HOH E:4428
BINDING SITE FOR RESIDUE CL E 3026
19
CC1
SOFTWARE
HOH D:4047 , HOH D:4048 , HOH E:4049 , HOH E:4050 , HOH E:4051 , HOH E:4052
BINDING SITE FOR RESIDUE MG D 3027
20
CC2
SOFTWARE
HOH E:4053 , HOH E:4054 , HOH E:4055 , HOH E:4056 , HOH E:4057 , HOH E:4058
BINDING SITE FOR RESIDUE MG E 3028
21
CC3
SOFTWARE
ARG F:137 , ARG F:138 , HOH F:4096
BINDING SITE FOR RESIDUE CL F 3030
22
CC4
SOFTWARE
GLY F:153 , GLY F:214 , HOH F:4254
BINDING SITE FOR RESIDUE CL F 3031
23
CC5
SOFTWARE
HOH E:4059 , HOH E:4060 , HOH E:4061 , HOH F:4006 , HOH F:4007 , HOH F:4008
BINDING SITE FOR RESIDUE MG E 3032
24
CC6
SOFTWARE
HOH F:4009 , HOH F:4010 , HOH F:4011 , HOH F:4012 , HOH F:4013 , HOH F:4014
BINDING SITE FOR RESIDUE MG F 3033
25
CC7
SOFTWARE
ALA A:186 , LYS A:187 , GLY A:190 , ALA A:191 , PRO A:192 , TYR A:193 , HOH A:4334
BINDING SITE FOR RESIDUE EDO A 3005
26
CC8
SOFTWARE
LYS A:187 , ASN A:188 , GLY A:190 , HOH A:4065 , HOH A:4178 , HOH A:4211
BINDING SITE FOR RESIDUE EDO A 3006
27
CC9
SOFTWARE
LYS B:187 , HOH B:4347 , LYS F:187 , ASN F:188 , LEU F:189 , GLY F:190
BINDING SITE FOR RESIDUE EDO B 3011
28
DC1
SOFTWARE
LYS B:187 , ALA B:191 , PRO B:192 , TYR B:193 , GLY F:190 , PRO F:192 , EDO F:3035
BINDING SITE FOR RESIDUE EDO B 3012
29
DC2
SOFTWARE
PRO C:192 , TYR C:193 , GLU C:194 , LEU C:195 , HOH C:4139 , HOH C:4214 , PRO E:192 , TYR E:193 , GLU E:194
BINDING SITE FOR RESIDUE EDO C 3017
30
DC3
SOFTWARE
ALA C:186 , LYS C:187 , ALA C:191 , PRO C:192 , TYR C:193 , GLY E:190 , PRO E:192
BINDING SITE FOR RESIDUE EDO C 3018
31
DC4
SOFTWARE
ASP C:24 , LYS C:81 , ASP C:102 , ARG C:147 , PHE C:233
BINDING SITE FOR RESIDUE EDO C 3019
32
DC5
SOFTWARE
ALA D:186 , LYS D:187 , GLY D:190 , ALA D:191 , PRO D:192 , TYR D:193
BINDING SITE FOR RESIDUE EDO D 3024
33
DC6
SOFTWARE
GLY C:190 , PRO C:192 , LYS E:187 , ALA E:191 , PRO E:192 , TYR E:193
BINDING SITE FOR RESIDUE EDO E 3029
34
DC7
SOFTWARE
PRO B:192 , TYR B:193 , GLU B:194 , PRO F:192 , TYR F:193 , GLU F:194 , LEU F:195 , HOH F:4158
BINDING SITE FOR RESIDUE EDO F 3034
35
DC8
SOFTWARE
GLY B:190 , ALA B:191 , PRO B:192 , EDO B:3012 , ALA F:186 , LYS F:187 , ALA F:191 , PRO F:192 , TYR F:193
BINDING SITE FOR RESIDUE EDO F 3035
[
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, 10)
Info
All PROSITE Patterns/Profiles
1: PDXS_SNZ_2 (A:9-271,C:9-271,D:9-272,E:9-270)
2: PDXS_SNZ_1 (A:205-223,B:205-223,C:205-223,D:20...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDXS_SNZ_2
PS51129
PdxS/SNZ family profile.
PDXS_BACSU
9-294
4
A:9-271
C:9-271
D:9-272
E:9-270
2
PDXS_SNZ_1
PS01235
PdxS/SNZ family signature.
PDXS_BACSU
205-223
6
A:205-223
B:205-223
C:205-223
D:205-223
E:205-223
F:205-223
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d2nv1a_ (A:)
1b: SCOP_d2nv1b_ (B:)
1c: SCOP_d2nv1c_ (C:)
1d: SCOP_d2nv1d_ (D:)
1e: SCOP_d2nv1e_ (E:)
1f: SCOP_d2nv1f_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Ribulose-phoshate binding barrel
(356)
Family
:
PdxS-like
(6)
Protein domain
:
automated matches
(5)
Bacillus subtilis [TaxId: 1423]
(2)
1a
d2nv1a_
A:
1b
d2nv1b_
B:
1c
d2nv1c_
C:
1d
d2nv1d_
D:
1e
d2nv1e_
E:
1f
d2nv1f_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_SOR_SNZ_2nv1F01 (F:12-212)
1b: PFAM_SOR_SNZ_2nv1F02 (F:12-212)
1c: PFAM_SOR_SNZ_2nv1F03 (F:12-212)
1d: PFAM_SOR_SNZ_2nv1F04 (F:12-212)
1e: PFAM_SOR_SNZ_2nv1F05 (F:12-212)
1f: PFAM_SOR_SNZ_2nv1F06 (F:12-212)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
SOR_SNZ
(6)
Bacillus subtilis
(2)
1a
SOR_SNZ-2nv1F01
F:12-212
1b
SOR_SNZ-2nv1F02
F:12-212
1c
SOR_SNZ-2nv1F03
F:12-212
1d
SOR_SNZ-2nv1F04
F:12-212
1e
SOR_SNZ-2nv1F05
F:12-212
1f
SOR_SNZ-2nv1F06
F:12-212
[
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
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 (288 KB)
Header - Asym.Unit
Biol.Unit 1 (549 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
2NV1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help