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.
1NF6
Biol. Unit 10
Info
Asym.Unit (500 KB)
Biol.Unit 1 (725 KB)
Biol.Unit 10 (66 KB)
Biol.Unit 2 (717 KB)
Biol.Unit 3 (67 KB)
Biol.Unit 4 (66 KB)
Biol.Unit 5 (66 KB)
Biol.Unit 6 (67 KB)
Biol.Unit 7 (67 KB)
Biol.Unit 8 (67 KB)
Biol.Unit 9 (65 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF THE DESULFOVIBRIO DESULFURICANS BACTERIOFERRITIN: THE DIIRON SITE IN DIFFERENT CATALYTIC STATES ("CYCLED" STRUCTURE: REDUCED IN SOLUTION AND ALLOWED TO REOXIDISE BEFORE CRYSTALLISATION)
Authors
:
S. Macedo, C. V. Romao, E. Mitchell, P. M. Matias, M. Y. Liu, A. V. Xavier, M. Teixeira, P. Lindley, M. A. Carrondo
Date
:
13 Dec 02 (Deposition) - 01 Apr 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,G,H,I,J,M,N (3x)
Biol. Unit 2: C,D,E,F,K,L,O,P (3x)
Biol. Unit 3: M,N (1x)
Biol. Unit 4: E,F (1x)
Biol. Unit 5: C,D (1x)
Biol. Unit 6: I,J (1x)
Biol. Unit 7: K,L (1x)
Biol. Unit 8: G,H (1x)
Biol. Unit 9: O,P (1x)
Biol. Unit 10: A,B (1x)
Keywords
:
Bacterioferritin, 24 Subunits In The Active Molecule, Diiron Centre, Haem Fe-Coproporphyrin Iii Cofactor, Iron Storage-Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Macedo, C. V. Romao, E. Mitchell, P. M. Matias, M. Y. Liu, A. V. Xavier J. Legall, M. Teixeira, P. Lindley, M. A. Carrondo
The Nature Of The Di-Iron Site In The Bacterioferritin From Desulfovibrio Desulfuricans
Nat. Struct. Biol. V. 10 285 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 5)
Info
All Hetero Components
2a: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECa)
2b: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECb)
2c: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECc)
2d: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECd)
2e: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECe)
2f: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECf)
2g: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECg)
2h: 1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6... (FECh)
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
2e: FE (III) ION (FEe)
2f: FE (III) ION (FEf)
2g: FE (III) ION (FEg)
2h: FE (III) ION (FEh)
2i: FE (III) ION (FEi)
2j: FE (III) ION (FEj)
2k: FE (III) ION (FEk)
2l: FE (III) ION (FEl)
2m: FE (III) ION (FEm)
2n: FE (III) ION (FEn)
2o: FE (III) ION (FEo)
2p: FE (III) ION (FEp)
3a: GLYCEROL (GOLa)
4a: SULFATE ION (SO4a)
4aa: SULFATE ION (SO4aa)
4ab: SULFATE ION (SO4ab)
4ac: SULFATE ION (SO4ac)
4ad: SULFATE ION (SO4ad)
4ae: SULFATE ION (SO4ae)
4af: SULFATE ION (SO4af)
4ag: SULFATE ION (SO4ag)
4ah: SULFATE ION (SO4ah)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
4r: SULFATE ION (SO4r)
4s: SULFATE ION (SO4s)
4t: SULFATE ION (SO4t)
4u: SULFATE ION (SO4u)
4v: SULFATE ION (SO4v)
4w: SULFATE ION (SO4w)
4x: SULFATE ION (SO4x)
4y: SULFATE ION (SO4y)
4z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
-1
Ligand/Ion
FE (III) ION
2
FEC
1
Ligand/Ion
1,3,5,8-TETRAMETHYL-PORPHINE-2,4,6,7-TETRAPROPIONICACID FERROUS COMPLEX
3
GOL
-1
Ligand/Ion
GLYCEROL
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: FC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:56 , GLU A:99 , GLU A:132 , HIS A:135
BINDING SITE FOR RESIDUE FE A 200
2
AC2
SOFTWARE
LYS A:50 , SER A:162 , THR A:164 , GLY A:165
BINDING SITE FOR RESIDUE SO4 A 1001
3
AC3
SOFTWARE
SER A:144 , ASN A:148
BINDING SITE FOR RESIDUE SO4 A 1003
4
AC4
SOFTWARE
LYS A:114 , HOH A:1109
BINDING SITE FOR RESIDUE SO4 A 1004
5
AC5
SOFTWARE
GLU B:56 , GLU B:99 , GLU B:132 , HIS B:135
BINDING SITE FOR RESIDUE FE B 200
6
AC6
SOFTWARE
FEC A:1005 , LYS B:50 , THR B:164 , HOH B:1279 , HOH B:1313
BINDING SITE FOR RESIDUE SO4 B 1201
7
AC7
SOFTWARE
LYS B:114 , LYS G:114 , LYS N:114
BINDING SITE FOR RESIDUE SO4 N 1204
8
FC6
SOFTWARE
ARG A:20 , MET A:31 , TYR A:35 , LYS A:50 , MET A:57 , GLU A:61 , SER A:168 , LYS A:169 , HOH A:1016 , HOH A:1018 , HOH A:1098 , HOH A:1119 , HOH A:1122 , ARG B:20 , HIS B:28 , MET B:31 , TYR B:35 , LYS B:50 , MET B:57 , GLU B:61 , ALA B:167 , SER B:168 , SO4 B:1201
BINDING SITE FOR RESIDUE FEC A 1005
[
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
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: FERRITIN_LIKE (A:6-150,B:6-150)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FERRITIN_LIKE
PS50905
Ferritin-like diiron domain profile.
BFR_DESDA
6-150
2
A:6-150
B:6-150
-
-
-
-
-
-
-
-
-
-
-
-
-
-
[
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
(1, 16)
Info
All SCOP Domains
1a: SCOP_d1nf6a_ (A:)
1b: SCOP_d1nf6b_ (B:)
1c: SCOP_d1nf6c_ (C:)
1d: SCOP_d1nf6d_ (D:)
1e: SCOP_d1nf6e_ (E:)
1f: SCOP_d1nf6f_ (F:)
1g: SCOP_d1nf6g_ (G:)
1h: SCOP_d1nf6h_ (H:)
1i: SCOP_d1nf6i_ (I:)
1j: SCOP_d1nf6j_ (J:)
1k: SCOP_d1nf6k_ (K:)
1l: SCOP_d1nf6l_ (L:)
1m: SCOP_d1nf6m_ (M:)
1n: SCOP_d1nf6n_ (N:)
1o: SCOP_d1nf6o_ (O:)
1p: SCOP_d1nf6p_ (P:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
Bacterioferritin (cytochrome b1)
(19)
Desulfovibrio desulfuricans [TaxId: 876]
(3)
1a
d1nf6a_
A:
1b
d1nf6b_
B:
1c
d1nf6c_
C:
1d
d1nf6d_
D:
1e
d1nf6e_
E:
1f
d1nf6f_
F:
1g
d1nf6g_
G:
1h
d1nf6h_
H:
1i
d1nf6i_
I:
1j
d1nf6j_
J:
1k
d1nf6k_
K:
1l
d1nf6l_
L:
1m
d1nf6m_
M:
1n
d1nf6n_
N:
1o
d1nf6o_
O:
1p
d1nf6p_
P:
[
close SCOP info
]
CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_1nf6G00 (G:4-172)
1b: CATH_1nf6K00 (K:4-172)
1c: CATH_1nf6M00 (M:4-172)
1d: CATH_1nf6O00 (O:5-173)
1e: CATH_1nf6A00 (A:3-172)
1f: CATH_1nf6B00 (B:3-172)
1g: CATH_1nf6C00 (C:3-172)
1h: CATH_1nf6D00 (D:3-172)
1i: CATH_1nf6E00 (E:3-172)
1j: CATH_1nf6H00 (H:3-172)
1k: CATH_1nf6I00 (I:3-172)
1l: CATH_1nf6J00 (J:3-172)
1m: CATH_1nf6L00 (L:3-172)
1n: CATH_1nf6N00 (N:3-172)
1o: CATH_1nf6P00 (P:3-172)
1p: CATH_1nf6F00 (F:2-172)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Desulfovibrio desulfuricans. Organism_taxid: 876. Strain: atcc 27774
(3)
1a
1nf6G00
G:4-172
1b
1nf6K00
K:4-172
1c
1nf6M00
M:4-172
1d
1nf6O00
O:5-173
1e
1nf6A00
A:3-172
1f
1nf6B00
B:3-172
1g
1nf6C00
C:3-172
1h
1nf6D00
D:3-172
1i
1nf6E00
E:3-172
1j
1nf6H00
H:3-172
1k
1nf6I00
I:3-172
1l
1nf6J00
J:3-172
1m
1nf6L00
L:3-172
1n
1nf6N00
N:3-172
1o
1nf6P00
P:3-172
1p
1nf6F00
F:2-172
[
close CATH info
]
Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_Ferritin_1nf6P01 (P:13-149)
1b: PFAM_Ferritin_1nf6P02 (P:13-149)
1c: PFAM_Ferritin_1nf6P03 (P:13-149)
1d: PFAM_Ferritin_1nf6P04 (P:13-149)
1e: PFAM_Ferritin_1nf6P05 (P:13-149)
1f: PFAM_Ferritin_1nf6P06 (P:13-149)
1g: PFAM_Ferritin_1nf6P07 (P:13-149)
1h: PFAM_Ferritin_1nf6P08 (P:13-149)
1i: PFAM_Ferritin_1nf6P09 (P:13-149)
1j: PFAM_Ferritin_1nf6P10 (P:13-149)
1k: PFAM_Ferritin_1nf6P11 (P:13-149)
1l: PFAM_Ferritin_1nf6P12 (P:13-149)
1m: PFAM_Ferritin_1nf6P13 (P:13-149)
1n: PFAM_Ferritin_1nf6P14 (P:13-149)
1o: PFAM_Ferritin_1nf6P15 (P:13-149)
1p: PFAM_Ferritin_1nf6P16 (P:13-149)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
(3)
1a
Ferritin-1nf6P01
P:13-149
1b
Ferritin-1nf6P02
P:13-149
1c
Ferritin-1nf6P03
P:13-149
1d
Ferritin-1nf6P04
P:13-149
1e
Ferritin-1nf6P05
P:13-149
1f
Ferritin-1nf6P06
P:13-149
1g
Ferritin-1nf6P07
P:13-149
1h
Ferritin-1nf6P08
P:13-149
1i
Ferritin-1nf6P09
P:13-149
1j
Ferritin-1nf6P10
P:13-149
1k
Ferritin-1nf6P11
P:13-149
1l
Ferritin-1nf6P12
P:13-149
1m
Ferritin-1nf6P13
P:13-149
1n
Ferritin-1nf6P14
P:13-149
1o
Ferritin-1nf6P15
P:13-149
1p
Ferritin-1nf6P16
P:13-149
[
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
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 (500 KB)
Header - Asym.Unit
Biol.Unit 1 (725 KB)
Header - Biol.Unit 1
Biol.Unit 10 (66 KB)
Header - Biol.Unit 10
Biol.Unit 2 (717 KB)
Header - Biol.Unit 2
Biol.Unit 3 (67 KB)
Header - Biol.Unit 3
Biol.Unit 4 (66 KB)
Header - Biol.Unit 4
Biol.Unit 5 (66 KB)
Header - Biol.Unit 5
Biol.Unit 6 (67 KB)
Header - Biol.Unit 6
Biol.Unit 7 (67 KB)
Header - Biol.Unit 7
Biol.Unit 8 (67 KB)
Header - Biol.Unit 8
Biol.Unit 9 (65 KB)
Header - Biol.Unit 9
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
1NF6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help