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1M1Y
Biol. Unit 1
Info
Asym.Unit (936 KB)
Biol.Unit 1 (467 KB)
Biol.Unit 2 (468 KB)
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(1)
Title
:
CHEMICAL CROSSLINK OF NITROGENASE MOFE PROTEIN AND FE PROTEIN
Authors
:
B. Schmid, O. Einsle, H. J. Chiu, A. Willing, M. Yoshida, J. B. Howard, D. C. Rees
Date
:
20 Jun 02 (Deposition) - 11 Feb 03 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: I,J,K,L,M,N,O,P (1x)
Keywords
:
Nitrogenase, Nitrogen Fixation, Chemical Crosslink, Protein Interaction, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Schmid, O. Einsle, H. J. Chiu, A. Willing, M. Yoshida, J. B. Howard, D. C. Rees
Biochemical And Structural Characterization Of The Crosslinked Complex Of Nitrogenase: Comparison To The Adp-Alf4- Stabilized Structure
Biochemistry V. 41 15557 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: FE-MO-S CLUSTER (CFMa)
2b: FE-MO-S CLUSTER (CFMb)
2c: FE-MO-S CLUSTER (CFMc)
2d: FE-MO-S CLUSTER (CFMd)
3a: FE(8)-S(7) CLUSTER (CLFa)
3b: FE(8)-S(7) CLUSTER (CLFb)
3c: FE(8)-S(7) CLUSTER (CLFc)
3d: FE(8)-S(7) CLUSTER (CLFd)
4a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
4b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
4c: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAc)
4d: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAd)
5a: IRON/SULFUR CLUSTER (SF4a)
5b: IRON/SULFUR CLUSTER (SF4b)
5c: IRON/SULFUR CLUSTER (SF4c)
5d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CFM
2
Ligand/Ion
FE-MO-S CLUSTER
3
CLF
2
Ligand/Ion
FE(8)-S(7) CLUSTER
4
HCA
2
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
5
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:108 , GLU B:109 , ASP D:353 , ASP D:357
BINDING SITE FOR RESIDUE CA D 6492
02
AC2
SOFTWARE
ASP B:353 , ASP B:357 , ARG D:108 , GLU D:109
BINDING SITE FOR RESIDUE CA B 7492
03
AC5
SOFTWARE
GLN A:191 , GLY A:424 , ILE A:425 , LYS A:426 , HIS A:442 , CFM A:6496
BINDING SITE FOR RESIDUE HCA A 6494
04
AC6
SOFTWARE
ARG A:96 , HIS A:195 , TYR A:229 , ILE A:231 , CYS A:275 , GLY A:356 , GLY A:357 , PHE A:381 , HIS A:442 , HCA A:6494
BINDING SITE FOR RESIDUE CFM A 6496
05
AC7
SOFTWARE
CYS A:62 , TYR A:64 , GLY A:87 , CYS A:88 , CYS A:154 , CYS B:70 , SER B:92 , CYS B:95 , THR B:152 , CYS B:153 , SER B:188
BINDING SITE FOR RESIDUE CLF A 6498
06
AC8
SOFTWARE
ALA C:65 , GLN C:191 , GLY C:424 , ILE C:425 , LYS C:426 , HIS C:442 , CFM C:7496
BINDING SITE FOR RESIDUE HCA C 7494
07
AC9
SOFTWARE
ARG C:96 , HIS C:195 , TYR C:229 , CYS C:275 , SER C:278 , ILE C:355 , GLY C:356 , GLY C:357 , PHE C:381 , HIS C:442 , HCA C:7494
BINDING SITE FOR RESIDUE CFM C 7496
08
BC1
SOFTWARE
CYS C:62 , TYR C:64 , GLY C:87 , CYS C:88 , CYS C:154 , CYS D:70 , SER D:92 , CYS D:95 , THR D:152 , CYS D:153 , SER D:188
BINDING SITE FOR RESIDUE CLF D 7498
09
BC2
SOFTWARE
CYS E:97 , ALA E:98 , CYS E:132 , GLY E:133 , GLY E:134 , CYS F:97 , ALA F:98 , CYS F:132 , GLY F:134
BINDING SITE FOR RESIDUE SF4 E 290
10
BC3
SOFTWARE
CYS G:97 , ALA G:98 , CYS G:132 , GLY G:134 , CYS H:97 , ALA H:98 , CYS H:132 , GLY H:134
BINDING SITE FOR RESIDUE SF4 G 1290
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(5, 20)
Info
All PROSITE Patterns/Profiles
1: NIFH_FRXC_3 (E:2-274,F:2-274,G:2-274,H:2-274)
2: NITROGENASE_1_1 (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)
;
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:2-274
F:2-274
G:2-274
H:2-274
-
-
-
-
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
-
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 16)
Info
All SCOP Domains
1a: SCOP_d1m1ya_ (A:)
1b: SCOP_d1m1yc_ (C:)
1c: SCOP_d1m1yi_ (I:)
1d: SCOP_d1m1yk_ (K:)
2a: SCOP_d1m1yb_ (B:)
2b: SCOP_d1m1yd_ (D:)
2c: SCOP_d1m1yj_ (J:)
2d: SCOP_d1m1yl_ (L:)
3a: SCOP_d1m1ye_ (E:)
3b: SCOP_d1m1yf_ (F:)
3c: SCOP_d1m1yg_ (G:)
3d: SCOP_d1m1yh_ (H:)
3e: SCOP_d1m1ym_ (M:)
3f: SCOP_d1m1yn_ (N:)
3g: SCOP_d1m1yo_ (O:)
3h: SCOP_d1m1yp_ (P:)
View:
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)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
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
d1m1ya_
A:
1b
d1m1yc_
C:
1c
d1m1yi_
I:
1d
d1m1yk_
K:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Azotobacter vinelandii [TaxId: 354]
(15)
2a
d1m1yb_
B:
2b
d1m1yd_
D:
2c
d1m1yj_
J:
2d
d1m1yl_
L:
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
d1m1ye_
E:
3b
d1m1yf_
F:
3c
d1m1yg_
G:
3d
d1m1yh_
H:
3e
d1m1ym_
M:
3f
d1m1yn_
N:
3g
d1m1yo_
O:
3h
d1m1yp_
P:
[
close SCOP info
]
CATH Domains
(3, 36)
Info
all CATH domains
1a: CATH_1m1yA02 (A:63-205)
1b: CATH_1m1yB02 (B:216-320)
1c: CATH_1m1yD02 (D:216-320)
1d: CATH_1m1yJ02 (J:216-320)
1e: CATH_1m1yL02 (L:216-320)
1f: CATH_1m1yA01 (A:4-62,A:345-479)
1g: CATH_1m1yC01 (C:4-62,C:345-479)
1h: CATH_1m1yI01 (I:4-62,I:345-479)
1i: CATH_1m1yK01 (K:4-62,K:345-479)
1j: CATH_1m1yC02 (C:63-205)
1k: CATH_1m1yI02 (I:63-205)
1l: CATH_1m1yK02 (K:63-205)
1m: CATH_1m1yB01 (B:70-215)
1n: CATH_1m1yD01 (D:70-215)
1o: CATH_1m1yJ01 (J:70-215)
1p: CATH_1m1yL01 (L:70-215)
1q: CATH_1m1yA03 (A:206-320)
1r: CATH_1m1yC03 (C:206-320)
1s: CATH_1m1yI03 (I:206-320)
1t: CATH_1m1yK03 (K:206-320)
1u: CATH_1m1yB04 (B:365-470)
1v: CATH_1m1yD04 (D:365-470)
1w: CATH_1m1yJ04 (J:365-470)
1x: CATH_1m1yL04 (L:365-470)
2a: CATH_1m1yE00 (E:1-286)
2b: CATH_1m1yG00 (G:1-286)
2c: CATH_1m1yM00 (M:1-286)
2d: CATH_1m1yO00 (O:1-286)
2e: CATH_1m1yF00 (F:1-289)
2f: CATH_1m1yH00 (H:1-289)
2g: CATH_1m1yN00 (N:1-289)
2h: CATH_1m1yP00 (P:1-289)
3a: CATH_1m1yB03 (B:321-364,B:485-523)
3b: CATH_1m1yD03 (D:321-364,D:485-523)
3c: CATH_1m1yJ03 (J:321-364,J:485-523)
3d: CATH_1m1yL03 (L:321-364,L:485-523)
View:
Select:
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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
1m1yA02
A:63-205
1b
1m1yB02
B:216-320
1c
1m1yD02
D:216-320
1d
1m1yJ02
J:216-320
1e
1m1yL02
L:216-320
1f
1m1yA01
A:4-62,A:345-479
1g
1m1yC01
C:4-62,C:345-479
1h
1m1yI01
I:4-62,I:345-479
1i
1m1yK01
K:4-62,K:345-479
1j
1m1yC02
C:63-205
1k
1m1yI02
I:63-205
1l
1m1yK02
K:63-205
1m
1m1yB01
B:70-215
1n
1m1yD01
D:70-215
1o
1m1yJ01
J:70-215
1p
1m1yL01
L:70-215
1q
1m1yA03
A:206-320
1r
1m1yC03
C:206-320
1s
1m1yI03
I:206-320
1t
1m1yK03
K:206-320
1u
1m1yB04
B:365-470
1v
1m1yD04
D:365-470
1w
1m1yJ04
J:365-470
1x
1m1yL04
L:365-470
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
2a
1m1yE00
E:1-286
2b
1m1yG00
G:1-286
2c
1m1yM00
M:1-286
2d
1m1yO00
O:1-286
2e
1m1yF00
F:1-289
2f
1m1yH00
H:1-289
2g
1m1yN00
N:1-289
2h
1m1yP00
P:1-289
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
1m1yB03
B:321-364,B:485-523
3b
1m1yD03
D:321-364,D:485-523
3c
1m1yJ03
J:321-364,J:485-523
3d
1m1yL03
L:321-364,L:485-523
[
close CATH info
]
Pfam Domains
(3, 20)
Info
all PFAM domains
1a: PFAM_Fer4_NifH_1m1yP01 (P:3-275)
1b: PFAM_Fer4_NifH_1m1yP02 (P:3-275)
1c: PFAM_Fer4_NifH_1m1yP03 (P:3-275)
1d: PFAM_Fer4_NifH_1m1yP04 (P:3-275)
1e: PFAM_Fer4_NifH_1m1yP05 (P:3-275)
1f: PFAM_Fer4_NifH_1m1yP06 (P:3-275)
1g: PFAM_Fer4_NifH_1m1yP07 (P:3-275)
1h: PFAM_Fer4_NifH_1m1yP08 (P:3-275)
2a: PFAM_DUF3364_1m1yL01 (L:2-56)
2b: PFAM_DUF3364_1m1yL02 (L:2-56)
2c: PFAM_DUF3364_1m1yL03 (L:2-56)
2d: PFAM_DUF3364_1m1yL04 (L:2-56)
3a: PFAM_Oxidored_nitro_1m1yK01 (K:62-468)
3b: PFAM_Oxidored_nitro_1m1yK02 (K:62-468)
3c: PFAM_Oxidored_nitro_1m1yK03 (K:62-468)
3d: PFAM_Oxidored_nitro_1m1yK04 (K:62-468)
3e: PFAM_Oxidored_nitro_1m1yL05 (L:70-502)
3f: PFAM_Oxidored_nitro_1m1yL06 (L:70-502)
3g: PFAM_Oxidored_nitro_1m1yL07 (L:70-502)
3h: PFAM_Oxidored_nitro_1m1yL08 (L:70-502)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Fer4_NifH
(10)
Azotobacter vinelandii
(10)
1a
Fer4_NifH-1m1yP01
P:3-275
1b
Fer4_NifH-1m1yP02
P:3-275
1c
Fer4_NifH-1m1yP03
P:3-275
1d
Fer4_NifH-1m1yP04
P:3-275
1e
Fer4_NifH-1m1yP05
P:3-275
1f
Fer4_NifH-1m1yP06
P:3-275
1g
Fer4_NifH-1m1yP07
P:3-275
1h
Fer4_NifH-1m1yP08
P:3-275
Clan
:
no clan defined [family: DUF3364]
(10)
Family
:
DUF3364
(10)
Azotobacter vinelandii
(8)
2a
DUF3364-1m1yL01
L:2-56
2b
DUF3364-1m1yL02
L:2-56
2c
DUF3364-1m1yL03
L:2-56
2d
DUF3364-1m1yL04
L:2-56
Clan
:
no clan defined [family: Oxidored_nitro]
(12)
Family
:
Oxidored_nitro
(12)
Azotobacter vinelandii
(8)
3a
Oxidored_nitro-1m1yK01
K:62-468
3b
Oxidored_nitro-1m1yK02
K:62-468
3c
Oxidored_nitro-1m1yK03
K:62-468
3d
Oxidored_nitro-1m1yK04
K:62-468
3e
Oxidored_nitro-1m1yL05
L:70-502
3f
Oxidored_nitro-1m1yL06
L:70-502
3g
Oxidored_nitro-1m1yL07
L:70-502
3h
Oxidored_nitro-1m1yL08
L:70-502
[
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]
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