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1FP6
Asym. Unit
Info
Asym.Unit (209 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (103 KB)
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(1)
Title
:
THE NITROGENASE FE PROTEIN FROM AZOTOBACTER VINELANDII COMPLEXED WITH MGADP
Authors
:
S. B. Jang, L. C. Seefeldt, J. W. Peters
Date
:
30 Aug 00 (Deposition) - 17 Jan 01 (Release) - 31 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Nitrogenase, Nitrogen Fixation, Nuclotide, Mgadp, Fe Protein, Av2, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. B. Jang, L. C. Seefeldt, J. W. Peters
Insights Into Nucleotide Signal Transduction In Nitrogenase: Structure Of An Iron Protein With Mgadp Bound.
Biochemistry V. 39 14745 2000
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: IRON/SULFUR CLUSTER (SF4a)
3b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:16 , ADP A:5291 , HOH A:5436 , HOH A:5447 , HOH A:5457 , HOH A:5504
BINDING SITE FOR RESIDUE MG A 5292
02
AC2
SOFTWARE
SER B:16 , ADP B:6291 , HOH B:6433 , HOH B:6439 , HOH B:6450 , HOH B:6483
BINDING SITE FOR RESIDUE MG B 6292
03
AC3
SOFTWARE
SER C:16 , ADP C:7291 , HOH C:7450 , HOH C:7453 , HOH C:7490 , HOH C:7504
BINDING SITE FOR RESIDUE MG C 7292
04
AC4
SOFTWARE
SER D:16 , ASP D:43 , ADP D:8291 , HOH D:8401 , HOH D:8402 , HOH D:8415 , HOH D:8433
BINDING SITE FOR RESIDUE MG D 8292
05
AC5
SOFTWARE
CYS A:97 , CYS A:132 , CYS B:97 , ALA B:98 , CYS B:132
BINDING SITE FOR RESIDUE SF4 A 5290
06
AC6
SOFTWARE
CYS C:97 , CYS C:132 , GLY C:133 , CYS D:97 , ALA D:98 , CYS D:132 , GLY D:133
BINDING SITE FOR RESIDUE SF4 C 7290
07
AC7
SOFTWARE
GLY A:12 , ILE A:13 , GLY A:14 , LYS A:15 , SER A:16 , THR A:17 , ASN A:185 , PRO A:212 , ARG A:213 , ASP A:214 , VAL A:217 , GLN A:218 , GLU A:221 , GLN A:236 , MG A:5292 , HOH A:5301 , HOH A:5350 , HOH A:5408 , HOH A:5436 , HOH A:5447 , HOH A:5457
BINDING SITE FOR RESIDUE ADP A 5291
08
AC8
SOFTWARE
LYS B:10 , GLY B:12 , ILE B:13 , GLY B:14 , LYS B:15 , SER B:16 , THR B:17 , ASN B:185 , PRO B:212 , ARG B:213 , ASP B:214 , GLN B:218 , GLU B:221 , GLN B:236 , TYR B:240 , MG B:6292 , HOH B:6318 , HOH B:6325 , HOH B:6376 , HOH B:6433 , HOH B:6447 , HOH B:6450 , HOH B:6470 , HOH B:6483
BINDING SITE FOR RESIDUE ADP B 6291
09
AC9
SOFTWARE
LYS C:10 , GLY C:12 , ILE C:13 , GLY C:14 , LYS C:15 , SER C:16 , THR C:17 , ASN C:185 , VAL C:211 , PRO C:212 , ARG C:213 , ASP C:214 , GLN C:218 , GLU C:221 , GLN C:236 , TYR C:240 , MG C:7292 , HOH C:7305 , HOH C:7418 , HOH C:7422 , HOH C:7429 , HOH C:7441 , HOH C:7453 , HOH C:7490 , HOH C:7504 , HOH C:7536
BINDING SITE FOR RESIDUE ADP C 7291
10
BC1
SOFTWARE
GLY D:12 , ILE D:13 , GLY D:14 , LYS D:15 , SER D:16 , THR D:17 , ASN D:185 , PRO D:212 , ARG D:213 , ASP D:214 , VAL D:217 , GLN D:218 , GLU D:221 , GLN D:236 , MG D:8292 , HOH D:8327 , HOH D:8401 , HOH D:8415 , HOH D:8433 , HOH D:8448
BINDING SITE FOR RESIDUE ADP D 8291
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: NIFH_FRXC_3 (A:2-274,B:2-274,C:2-274,D:2-274)
2: NIFH_FRXC_1 (A:87-99,B:87-99,C:87-99,D:87-99)
3: NIFH_FRXC_2 (A:125-138,B:125-138,C:125-138,D:12...)
;
View:
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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
A:2-274
B:2-274
C:2-274
D:2-274
2
NIFH_FRXC_1
PS00746
NifH/frxC family signature 1.
NIFH1_AZOVI
88-100
4
A:87-99
B:87-99
C:87-99
D:87-99
3
NIFH_FRXC_2
PS00692
NifH/frxC family signature 2.
NIFH1_AZOVI
126-139
4
A:125-138
B:125-138
C:125-138
D:125-138
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1fp6a_ (A:)
1b: SCOP_d1fp6b_ (B:)
1c: SCOP_d1fp6c_ (C:)
1d: SCOP_d1fp6d_ (D:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
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)
1a
d1fp6a_
A:
1b
d1fp6b_
B:
1c
d1fp6c_
C:
1d
d1fp6d_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1fp6C00 (C:1-285)
1b: CATH_1fp6D00 (D:1-285)
1c: CATH_1fp6A00 (A:1-289)
1d: CATH_1fp6B00 (B:1-289)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Azotobacter vinelandii. Organism_taxid: 354.
(5)
1a
1fp6C00
C:1-285
1b
1fp6D00
D:1-285
1c
1fp6A00
A:1-289
1d
1fp6B00
B:1-289
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain D
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (209 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
Biol.Unit 2 (103 KB)
Header - Biol.Unit 2
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