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1YCE
Biol. Unit 1
Info
Asym.Unit (571 KB)
Biol.Unit 1 (143 KB)
Biol.Unit 2 (142 KB)
Biol.Unit 3 (145 KB)
Biol.Unit 4 (144 KB)
(using Jmol or JSmol)
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(1)
Title
:
STRUCTURE OF THE ROTOR RING OF F-TYPE NA+-ATPASE FROM ILYOBACTER TARTARICUS
Authors
:
T. Meier, P. Polzer, K. Diederichs, W. Welte, P. Dimroth
Date
:
22 Dec 04 (Deposition) - 12 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K (1x)
Biol. Unit 2: L,M,N,O,P,Q,R,S,T,U,V (1x)
Biol. Unit 3: a,b,c,d,e,f,g,h,i,j,k (1x)
Biol. Unit 4: l,m,n,o,p,q,r,s,t,u,v (1x)
Keywords
:
Atp Synthase, Na Binding Site, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Meier, P. Polzer, K. Diederichs, W. Welte, P. Dimroth
Structure Of The Rotor Ring Of F-Type Na+-Atpase From Ilyobacter Tartaricus.
Science V. 308 659 2005
[
close entry info
]
Hetero Components
(1, 11)
Info
All Hetero Components
1a: NONAN-1-OL (F09a)
1aa: NONAN-1-OL (F09aa)
1ab: NONAN-1-OL (F09ab)
1ac: NONAN-1-OL (F09ac)
1ad: NONAN-1-OL (F09ad)
1ae: NONAN-1-OL (F09ae)
1af: NONAN-1-OL (F09af)
1ag: NONAN-1-OL (F09ag)
1ah: NONAN-1-OL (F09ah)
1ai: NONAN-1-OL (F09ai)
1aj: NONAN-1-OL (F09aj)
1ak: NONAN-1-OL (F09ak)
1al: NONAN-1-OL (F09al)
1am: NONAN-1-OL (F09am)
1an: NONAN-1-OL (F09an)
1ao: NONAN-1-OL (F09ao)
1ap: NONAN-1-OL (F09ap)
1aq: NONAN-1-OL (F09aq)
1ar: NONAN-1-OL (F09ar)
1b: NONAN-1-OL (F09b)
1c: NONAN-1-OL (F09c)
1d: NONAN-1-OL (F09d)
1e: NONAN-1-OL (F09e)
1f: NONAN-1-OL (F09f)
1g: NONAN-1-OL (F09g)
1h: NONAN-1-OL (F09h)
1i: NONAN-1-OL (F09i)
1j: NONAN-1-OL (F09j)
1k: NONAN-1-OL (F09k)
1l: NONAN-1-OL (F09l)
1m: NONAN-1-OL (F09m)
1n: NONAN-1-OL (F09n)
1o: NONAN-1-OL (F09o)
1p: NONAN-1-OL (F09p)
1q: NONAN-1-OL (F09q)
1r: NONAN-1-OL (F09r)
1s: NONAN-1-OL (F09s)
1t: NONAN-1-OL (F09t)
1u: NONAN-1-OL (F09u)
1v: NONAN-1-OL (F09v)
1w: NONAN-1-OL (F09w)
1x: NONAN-1-OL (F09x)
1y: NONAN-1-OL (F09y)
1z: NONAN-1-OL (F09z)
2a: SODIUM ION (NAa)
2aa: SODIUM ION (NAaa)
2ab: SODIUM ION (NAab)
2ac: SODIUM ION (NAac)
2ad: SODIUM ION (NAad)
2ae: SODIUM ION (NAae)
2af: SODIUM ION (NAaf)
2ag: SODIUM ION (NAag)
2ah: SODIUM ION (NAah)
2ai: SODIUM ION (NAai)
2aj: SODIUM ION (NAaj)
2ak: SODIUM ION (NAak)
2al: SODIUM ION (NAal)
2am: SODIUM ION (NAam)
2an: SODIUM ION (NAan)
2ao: SODIUM ION (NAao)
2ap: SODIUM ION (NAap)
2aq: SODIUM ION (NAaq)
2ar: SODIUM ION (NAar)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
2i: SODIUM ION (NAi)
2j: SODIUM ION (NAj)
2k: SODIUM ION (NAk)
2l: SODIUM ION (NAl)
2m: SODIUM ION (NAm)
2n: SODIUM ION (NAn)
2o: SODIUM ION (NAo)
2p: SODIUM ION (NAp)
2q: SODIUM ION (NAq)
2r: SODIUM ION (NAr)
2s: SODIUM ION (NAs)
2t: SODIUM ION (NAt)
2u: SODIUM ION (NAu)
2v: SODIUM ION (NAv)
2w: SODIUM ION (NAw)
2x: SODIUM ION (NAx)
2y: SODIUM ION (NAy)
2z: SODIUM ION (NAz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F09
11
Ligand/Ion
NONAN-1-OL
2
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(13, 13)
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: EC9 (SOFTWARE)
13: FC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:32 , GLU A:65 , VAL K:63 , SER K:66
BINDING SITE FOR RESIDUE NA A 201
02
AC2
SOFTWARE
VAL A:63 , SER A:66 , GLN B:32 , GLU B:65
BINDING SITE FOR RESIDUE NA B 201
03
AC3
SOFTWARE
VAL B:63 , SER B:66 , GLN C:32 , GLU C:65
BINDING SITE FOR RESIDUE NA C 201
04
AC4
SOFTWARE
VAL C:63 , SER C:66 , GLN D:32 , GLU D:65
BINDING SITE FOR RESIDUE NA D 201
05
AC5
SOFTWARE
VAL D:63 , SER D:66 , GLN E:32 , GLU E:65
BINDING SITE FOR RESIDUE NA E 201
06
AC6
SOFTWARE
VAL E:63 , SER E:66 , GLN F:32 , GLU F:65
BINDING SITE FOR RESIDUE NA F 201
07
AC7
SOFTWARE
VAL F:63 , SER F:66 , GLN G:32 , GLU G:65
BINDING SITE FOR RESIDUE NA G 201
08
AC8
SOFTWARE
VAL G:63 , SER G:66 , GLN H:32 , GLU H:65
BINDING SITE FOR RESIDUE NA H 201
09
AC9
SOFTWARE
VAL H:63 , SER H:66 , GLN I:32 , GLU I:65
BINDING SITE FOR RESIDUE NA I 201
10
BC1
SOFTWARE
VAL I:63 , SER I:66 , GLN J:32 , GLU J:65
BINDING SITE FOR RESIDUE NA J 201
11
BC2
SOFTWARE
VAL J:63 , SER J:66 , GLN K:32 , GLU K:65
BINDING SITE FOR RESIDUE NA K 201
12
EC9
SOFTWARE
HOH C:319
BINDING SITE FOR RESIDUE F09 B 314
13
FC1
SOFTWARE
HOH A:334
BINDING SITE FOR RESIDUE F09 K 314
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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]
PROSITE Patterns/Profiles
(1, 11)
Info
All PROSITE Patterns/Profiles
1: ATPASE_C (A:44-65,B:44-65,C:44-65,D:44-65,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_C
PS00605
ATP synthase c subunit signature.
ATPL_ILYTA
44-65
11
A:44-65
B:44-65
C:44-65
D:44-65
E:44-65
F:44-65
G:44-65
H:44-65
I:44-65
J:44-65
K:44-65
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(1, 44)
Info
all CATH domains
1a: CATH_1yceA01 (A:1-82)
1b: CATH_1yceB01 (B:1-82)
1c: CATH_1yceK01 (K:1-82)
1d: CATH_1yceL01 (L:1-82)
1e: CATH_1yceM01 (M:1-82)
1f: CATH_1yceN01 (N:1-82)
1g: CATH_1yceO01 (O:1-82)
1h: CATH_1yceP01 (P:1-82)
1i: CATH_1yceQ01 (Q:1-82)
1j: CATH_1yceR01 (R:1-82)
1k: CATH_1yceS01 (S:1-82)
1l: CATH_1yceT01 (T:1-82)
1m: CATH_1yceC01 (C:1-82)
1n: CATH_1yceU01 (U:1-82)
1o: CATH_1yceV01 (V:1-82)
1p: CATH_1ycea01 (a:1-82)
1q: CATH_1yceb01 (b:1-82)
1r: CATH_1ycec01 (c:1-82)
1s: CATH_1yced01 (d:1-82)
1t: CATH_1ycee01 (e:1-82)
1u: CATH_1ycef01 (f:1-82)
1v: CATH_1yceg01 (g:1-82)
1w: CATH_1yceh01 (h:1-82)
1x: CATH_1yceD01 (D:1-82)
1y: CATH_1ycei01 (i:1-82)
1z: CATH_1ycej01 (j:1-82)
1aa: CATH_1ycek01 (k:1-82)
1ab: CATH_1ycel01 (l:1-82)
1ac: CATH_1ycem01 (m:1-82)
1ad: CATH_1ycen01 (n:1-82)
1ae: CATH_1yceo01 (o:1-82)
1af: CATH_1ycep01 (p:1-82)
1ag: CATH_1yceq01 (q:1-82)
1ah: CATH_1ycer01 (r:1-82)
1ai: CATH_1yceE01 (E:1-82)
1aj: CATH_1yces01 (s:1-82)
1ak: CATH_1ycet01 (t:1-82)
1al: CATH_1yceu01 (u:1-82)
1am: CATH_1ycev01 (v:1-82)
1an: CATH_1yceF01 (F:1-82)
1ao: CATH_1yceG01 (G:1-82)
1ap: CATH_1yceH01 (H:1-82)
1aq: CATH_1yceI01 (I:1-82)
1ar: CATH_1yceJ01 (J:1-82)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
F1FO ATP Synthase
(13)
Homologous Superfamily
:
F1FO ATP Synthase
(13)
Ilyobacter tartaricus. Organism_taxid: 167644
(1)
1a
1yceA01
A:1-82
1b
1yceB01
B:1-82
1c
1yceK01
K:1-82
1d
1yceL01
L:1-82
1e
1yceM01
M:1-82
1f
1yceN01
N:1-82
1g
1yceO01
O:1-82
1h
1yceP01
P:1-82
1i
1yceQ01
Q:1-82
1j
1yceR01
R:1-82
1k
1yceS01
S:1-82
1l
1yceT01
T:1-82
1m
1yceC01
C:1-82
1n
1yceU01
U:1-82
1o
1yceV01
V:1-82
1p
1ycea01
a:1-82
1q
1yceb01
b:1-82
1r
1ycec01
c:1-82
1s
1yced01
d:1-82
1t
1ycee01
e:1-82
1u
1ycef01
f:1-82
1v
1yceg01
g:1-82
1w
1yceh01
h:1-82
1x
1yceD01
D:1-82
1y
1ycei01
i:1-82
1z
1ycej01
j:1-82
1aa
1ycek01
k:1-82
1ab
1ycel01
l:1-82
1ac
1ycem01
m:1-82
1ad
1ycen01
n:1-82
1ae
1yceo01
o:1-82
1af
1ycep01
p:1-82
1ag
1yceq01
q:1-82
1ah
1ycer01
r:1-82
1ai
1yceE01
E:1-82
1aj
1yces01
s:1-82
1ak
1ycet01
t:1-82
1al
1yceu01
u:1-82
1am
1ycev01
v:1-82
1an
1yceF01
F:1-82
1ao
1yceG01
G:1-82
1ap
1yceH01
H:1-82
1aq
1yceI01
I:1-82
1ar
1yceJ01
J:1-82
[
close CATH info
]
Pfam Domains
(1, 44)
Info
all PFAM domains
1a: PFAM_ATP_synt_C_1ycev01 (v:13-81)
1b: PFAM_ATP_synt_C_1ycev02 (v:13-81)
1c: PFAM_ATP_synt_C_1ycev03 (v:13-81)
1d: PFAM_ATP_synt_C_1ycev04 (v:13-81)
1e: PFAM_ATP_synt_C_1ycev05 (v:13-81)
1f: PFAM_ATP_synt_C_1ycev06 (v:13-81)
1g: PFAM_ATP_synt_C_1ycev07 (v:13-81)
1h: PFAM_ATP_synt_C_1ycev08 (v:13-81)
1i: PFAM_ATP_synt_C_1ycev09 (v:13-81)
1j: PFAM_ATP_synt_C_1ycev10 (v:13-81)
1k: PFAM_ATP_synt_C_1ycev11 (v:13-81)
1l: PFAM_ATP_synt_C_1ycev12 (v:13-81)
1m: PFAM_ATP_synt_C_1ycev13 (v:13-81)
1n: PFAM_ATP_synt_C_1ycev14 (v:13-81)
1o: PFAM_ATP_synt_C_1ycev15 (v:13-81)
1p: PFAM_ATP_synt_C_1ycev16 (v:13-81)
1q: PFAM_ATP_synt_C_1ycev17 (v:13-81)
1r: PFAM_ATP_synt_C_1ycev18 (v:13-81)
1s: PFAM_ATP_synt_C_1ycev19 (v:13-81)
1t: PFAM_ATP_synt_C_1ycev20 (v:13-81)
1u: PFAM_ATP_synt_C_1ycev21 (v:13-81)
1v: PFAM_ATP_synt_C_1ycev22 (v:13-81)
1w: PFAM_ATP_synt_C_1ycev23 (v:13-81)
1x: PFAM_ATP_synt_C_1ycev24 (v:13-81)
1y: PFAM_ATP_synt_C_1ycev25 (v:13-81)
1z: PFAM_ATP_synt_C_1ycev26 (v:13-81)
1aa: PFAM_ATP_synt_C_1ycev27 (v:13-81)
1ab: PFAM_ATP_synt_C_1ycev28 (v:13-81)
1ac: PFAM_ATP_synt_C_1ycev29 (v:13-81)
1ad: PFAM_ATP_synt_C_1ycev30 (v:13-81)
1ae: PFAM_ATP_synt_C_1ycev31 (v:13-81)
1af: PFAM_ATP_synt_C_1ycev32 (v:13-81)
1ag: PFAM_ATP_synt_C_1ycev33 (v:13-81)
1ah: PFAM_ATP_synt_C_1ycev34 (v:13-81)
1ai: PFAM_ATP_synt_C_1ycev35 (v:13-81)
1aj: PFAM_ATP_synt_C_1ycev36 (v:13-81)
1ak: PFAM_ATP_synt_C_1ycev37 (v:13-81)
1al: PFAM_ATP_synt_C_1ycev38 (v:13-81)
1am: PFAM_ATP_synt_C_1ycev39 (v:13-81)
1an: PFAM_ATP_synt_C_1ycev40 (v:13-81)
1ao: PFAM_ATP_synt_C_1ycev41 (v:13-81)
1ap: PFAM_ATP_synt_C_1ycev42 (v:13-81)
1aq: PFAM_ATP_synt_C_1ycev43 (v:13-81)
1ar: PFAM_ATP_synt_C_1ycev44 (v:13-81)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: ATP-synt_C]
(9)
Family
:
ATP-synt_C
(9)
Ilyobacter tartaricus
(2)
1a
ATP-synt_C-1ycev01
v:13-81
1b
ATP-synt_C-1ycev02
v:13-81
1c
ATP-synt_C-1ycev03
v:13-81
1d
ATP-synt_C-1ycev04
v:13-81
1e
ATP-synt_C-1ycev05
v:13-81
1f
ATP-synt_C-1ycev06
v:13-81
1g
ATP-synt_C-1ycev07
v:13-81
1h
ATP-synt_C-1ycev08
v:13-81
1i
ATP-synt_C-1ycev09
v:13-81
1j
ATP-synt_C-1ycev10
v:13-81
1k
ATP-synt_C-1ycev11
v:13-81
1l
ATP-synt_C-1ycev12
v:13-81
1m
ATP-synt_C-1ycev13
v:13-81
1n
ATP-synt_C-1ycev14
v:13-81
1o
ATP-synt_C-1ycev15
v:13-81
1p
ATP-synt_C-1ycev16
v:13-81
1q
ATP-synt_C-1ycev17
v:13-81
1r
ATP-synt_C-1ycev18
v:13-81
1s
ATP-synt_C-1ycev19
v:13-81
1t
ATP-synt_C-1ycev20
v:13-81
1u
ATP-synt_C-1ycev21
v:13-81
1v
ATP-synt_C-1ycev22
v:13-81
1w
ATP-synt_C-1ycev23
v:13-81
1x
ATP-synt_C-1ycev24
v:13-81
1y
ATP-synt_C-1ycev25
v:13-81
1z
ATP-synt_C-1ycev26
v:13-81
1aa
ATP-synt_C-1ycev27
v:13-81
1ab
ATP-synt_C-1ycev28
v:13-81
1ac
ATP-synt_C-1ycev29
v:13-81
1ad
ATP-synt_C-1ycev30
v:13-81
1ae
ATP-synt_C-1ycev31
v:13-81
1af
ATP-synt_C-1ycev32
v:13-81
1ag
ATP-synt_C-1ycev33
v:13-81
1ah
ATP-synt_C-1ycev34
v:13-81
1ai
ATP-synt_C-1ycev35
v:13-81
1aj
ATP-synt_C-1ycev36
v:13-81
1ak
ATP-synt_C-1ycev37
v:13-81
1al
ATP-synt_C-1ycev38
v:13-81
1am
ATP-synt_C-1ycev39
v:13-81
1an
ATP-synt_C-1ycev40
v:13-81
1ao
ATP-synt_C-1ycev41
v:13-81
1ap
ATP-synt_C-1ycev42
v:13-81
1aq
ATP-synt_C-1ycev43
v:13-81
1ar
ATP-synt_C-1ycev44
v:13-81
[
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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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