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.
1G21
Asym. Unit
Info
Asym.Unit (503 KB)
Biol.Unit 1 (491 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTEIN COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFE PROTEIN
Authors
:
H. -J. Chiu, J. W. Peters, W. N. Lanzilotta, M. J. Ryle, L. C. Seefeldt, J. B. Howard, D. C. Rees
Date
:
16 Oct 00 (Deposition) - 31 Jan 01 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Nitrogen-Fixation, Fe Protein, Moefe Protein, P-Cluster, Femo Cofactor, 4Fe-4S, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Chiu, J. W. Peters, W. N. Lanzilotta, M. J. Ryle, L. C. Seefeldt, J. B. Howard, D. C. Rees
Mgatp-Bound And Nucleotide-Free Structures Of A Nitrogenase Protein Complex Between The Leu 127 Delta-Fe-Protein And The Mofe-Protein.
Biochemistry V. 40 641 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: FE-MO-S CLUSTER (CFMa)
3b: FE-MO-S CLUSTER (CFMb)
4a: FE(8)-S(7) CLUSTER (CLFa)
4b: FE(8)-S(7) CLUSTER (CLFb)
5a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
5b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
4
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
2
Ligand/Ion
CALCIUM ION
3
CFM
2
Ligand/Ion
FE-MO-S CLUSTER
4
CLF
2
Ligand/Ion
FE(8)-S(7) CLUSTER
5
HCA
2
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
6
MG
4
Ligand/Ion
MAGNESIUM ION
7
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER E:16 , ASP E:39 , ASP E:43 , ASP E:125 , ATP E:5292
BINDING SITE FOR RESIDUE MG E 293
02
AC2
SOFTWARE
SER F:16 , ASP F:125 , ATP F:6292
BINDING SITE FOR RESIDUE MG F 293
03
AC3
SOFTWARE
SER H:16 , ASP H:125 , ATP H:8292
BINDING SITE FOR RESIDUE MG G 293
04
AC4
SOFTWARE
SER G:16 , ASP G:125 , ATP G:7292
BINDING SITE FOR RESIDUE MG H 293
05
AC5
SOFTWARE
ARG B:108 , GLU B:109 , ASP D:353 , ASP D:357
BINDING SITE FOR RESIDUE CA B 2492
06
AC6
SOFTWARE
ASP B:353 , ASP B:357 , ARG D:108 , GLU D:109
BINDING SITE FOR RESIDUE CA D 4492
07
AC7
SOFTWARE
LEU A:158 , VAL B:157 , CYS E:97 , ALA E:98 , GLY E:99 , CYS E:132 , CYS F:97 , ALA F:98 , GLY F:99 , CYS F:132
BINDING SITE FOR RESIDUE SF4 F 5290
08
AC8
SOFTWARE
LEU C:158 , VAL D:157 , CYS G:97 , ALA G:98 , GLY G:99 , CYS G:132 , CYS H:97 , ALA H:98 , GLY H:99 , CYS H:132
BINDING SITE FOR RESIDUE SF4 G 7290
09
AC9
SOFTWARE
GLY E:11 , GLY E:12 , ILE E:13 , GLY E:14 , LYS E:15 , SER E:16 , THR E:17 , ASP E:39 , LYS E:41 , ASN E:185 , PRO E:212 , ASP E:214 , VAL E:217 , GLU E:221 , GLN E:236 , MG E:293 , LYS F:10 , MET F:156
BINDING SITE FOR RESIDUE ATP E 5292
10
BC1
SOFTWARE
MET E:156 , GLY F:11 , GLY F:12 , ILE F:13 , GLY F:14 , LYS F:15 , SER F:16 , THR F:17 , ASP F:39 , LYS F:41 , PRO F:212 , ARG F:213 , VAL F:217 , GLN F:218 , GLU F:221 , GLN F:236 , TYR F:240 , MG F:293
BINDING SITE FOR RESIDUE ATP F 6292
11
BC2
SOFTWARE
GLY G:11 , GLY G:12 , ILE G:13 , GLY G:14 , LYS G:15 , SER G:16 , THR G:17 , ASP G:39 , ASN G:185 , SER G:186 , PRO G:212 , ARG G:213 , VAL G:217 , GLU G:221 , GLN G:236 , TYR G:240 , LYS H:10 , MET H:156 , MG H:293
BINDING SITE FOR RESIDUE ATP G 7292
12
BC3
SOFTWARE
MET G:156 , MG G:293 , GLY H:11 , GLY H:12 , ILE H:13 , GLY H:14 , LYS H:15 , SER H:16 , THR H:17 , ASP H:39 , LYS H:41 , ASN H:185 , PRO H:212 , ARG H:213 , VAL H:217 , GLU H:221 , GLN H:236 , TYR H:240
BINDING SITE FOR RESIDUE ATP H 8292
13
BC4
SOFTWARE
GLN A:191 , GLY A:424 , ILE A:425 , LYS A:426 , HIS A:442 , CFM A:1496
BINDING SITE FOR RESIDUE HCA A 1494
14
BC5
SOFTWARE
ALA C:65 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , CFM C:3496
BINDING SITE FOR RESIDUE HCA C 3494
15
BC6
SOFTWARE
ARG A:96 , HIS A:195 , TYR A:229 , ILE A:231 , CYS A:275 , SER A:278 , ILE A:355 , GLY A:357 , LEU A:358 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:1494
BINDING SITE FOR RESIDUE CFM A 1496
16
BC7
SOFTWARE
VAL C:70 , ARG C:96 , HIS C:195 , TYR C:229 , ILE C:231 , CYS C:275 , SER C:278 , ILE C:355 , GLY C:356 , GLY C:357 , LEU C:358 , ARG C:359 , PHE C:381 , HIS C:442 , HCA C:3494
BINDING SITE FOR RESIDUE CFM C 3496
17
BC8
SOFTWARE
CYS A:62 , TYR A:64 , PRO A:85 , GLY A:87 , CYS A:88 , CYS A:154 , GLY A:185 , CYS B:70 , PRO B:72 , SER B:92 , CYS B:95 , CYS B:153 , SER B:188
BINDING SITE FOR RESIDUE CLF A 1498
18
BC9
SOFTWARE
CYS C:62 , TYR C:64 , GLY C:87 , CYS C:88 , CYS C:154 , GLY C:185 , CYS D:70 , PRO D:72 , SER D:92 , CYS D:95 , THR D:152 , CYS D:153 , SER D:188
BINDING SITE FOR RESIDUE CLF D 3498
[
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
(5, 20)
Info
All PROSITE Patterns/Profiles
1: NIFH_FRXC_3 (E:2-270,F:2-269,G:2-270,H:2-270)
2: NITROGENASE_1_1 (A:81-88,C:81-88,B:88-95,D:88-95)
3: NIFH_FRXC_1 (E:87-99,F:87-99,G:87-99,H:87-99)
4: NIFH_FRXC_2 (E:125-138,F:125-138,G:125-138,H:12...)
5: NITROGENASE_1_2 (B:151-165,D:151-165,A:152-166,C:15...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NIFH_FRXC_3
PS51026
NIFH_FRXC family profile.
NIFH1_AZOVI
3-275
4
E:2-270
F:2-269
G:2-270
H:2-270
2
NITROGENASE_1_1
PS00699
Nitrogenases component 1 alpha and beta subunits signature 1.
NIFD_AZOVI
81-88
2
A:81-88
C:81-88
NIFK_AZOVI
88-95
2
B:88-95
D:88-95
3
NIFH_FRXC_1
PS00746
NifH/frxC family signature 1.
NIFH1_AZOVI
88-100
4
E:87-99
F:87-99
G:87-99
H:87-99
4
NIFH_FRXC_2
PS00692
NifH/frxC family signature 2.
NIFH1_AZOVI
126-139
4
E:125-138
F:125-138
G:125-138
H:125-138
5
NITROGENASE_1_2
PS00090
Nitrogenases component 1 alpha and beta subunits signature 2.
NIFK_AZOVI
151-165
2
B:151-165
D:151-165
NIFD_AZOVI
152-166
2
A:152-166
C:152-166
[
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
(3, 8)
Info
All SCOP Domains
1a: SCOP_d1g21a_ (A:)
1b: SCOP_d1g21c_ (C:)
2a: SCOP_d1g21b_ (B:)
2b: SCOP_d1g21d_ (D:)
3a: SCOP_d1g21e_ (E:)
3b: SCOP_d1g21f_ (F:)
3c: SCOP_d1g21g_ (G:)
3d: SCOP_d1g21h_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Chelatase-like
(149)
Superfamily
:
Helical backbone metal receptor
(102)
Family
:
Nitrogenase iron-molybdenum protein
(41)
Protein domain
:
Nitrogenase iron-molybdenum protein, alpha chain
(15)
Azotobacter vinelandii [TaxId: 354]
(10)
1a
d1g21a_
A:
1b
d1g21c_
C:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Azotobacter vinelandii [TaxId: 354]
(15)
2a
d1g21b_
B:
2b
d1g21d_
D:
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Nitrogenase iron protein-like
(152)
Protein domain
:
Nitrogenase iron protein
(21)
Azotobacter vinelandii [TaxId: 354]
(20)
3a
d1g21e_
E:
3b
d1g21f_
F:
3c
d1g21g_
G:
3d
d1g21h_
H:
[
close SCOP info
]
CATH Domains
(3, 18)
Info
all CATH domains
1a: CATH_1g21A02 (A:63-205)
1b: CATH_1g21C02 (C:63-205)
1c: CATH_1g21A01 (A:5-62,A:345-479)
1d: CATH_1g21C01 (C:5-62,C:345-479)
1e: CATH_1g21B01 (B:70-215)
1f: CATH_1g21D01 (D:70-215)
1g: CATH_1g21A03 (A:206-320)
1h: CATH_1g21C03 (C:206-320)
1i: CATH_1g21B03 (B:365-470)
1j: CATH_1g21D03 (D:365-470)
1k: CATH_1g21B02 (B:216-320)
1l: CATH_1g21D02 (D:216-320)
2a: CATH_1g21F00 (F:2-269)
2b: CATH_1g21E00 (E:2-270)
2c: CATH_1g21G00 (G:2-270)
2d: CATH_1g21H00 (H:2-270)
3a: CATH_1g21B04 (B:321-364,B:485-523)
3b: CATH_1g21D04 (D:321-364,D:485-523)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nitrogenase molybdenum iron protein domain
(45)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
1a
1g21A02
A:63-205
1b
1g21C02
C:63-205
1c
1g21A01
A:5-62,A:345-479
1d
1g21C01
C:5-62,C:345-479
1e
1g21B01
B:70-215
1f
1g21D01
D:70-215
1g
1g21A03
A:206-320
1h
1g21C03
C:206-320
1i
1g21B03
B:365-470
1j
1g21D03
D:365-470
1k
1g21B02
B:216-320
1l
1g21D02
D:216-320
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
2a
1g21F00
F:2-269
2b
1g21E00
E:2-270
2c
1g21G00
G:2-270
2d
1g21H00
H:2-270
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Nitrogenase Molybdenum-iron Protein, subunit B; domain 4
(19)
Homologous Superfamily
:
Nitrogenase Molybdenum-iron Protein, subunit B, domain 4
(19)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
3a
1g21B04
B:321-364,B:485-523
3b
1g21D04
D:321-364,D:485-523
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain G
Chain H
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 (503 KB)
Header - Asym.Unit
Biol.Unit 1 (491 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
1G21
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help