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2AFI
Biol. Unit 2
Info
Asym.Unit (994 KB)
Biol.Unit 1 (497 KB)
Biol.Unit 2 (495 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MGADP BOUND AV2-AV1 COMPLEX
Authors
:
F. A. Tezcan, J. T. Kaiser, D. Mustafi, M. Y. Walton, J. B. Howard, D. C. Rees
Date
:
25 Jul 05 (Deposition) - 06 Sep 05 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
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
:
Nitrogen Fixation, Iron-Sulfur, Metal-Binding, Molybdenum, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. A. Tezcan, J. T. Kaiser, D. Mustafi, M. Y. Walton, J. B. Howard, D. C. Rees
Nitrogenase Complexes: Multiple Docking Sites For A Nucleotide Switch Protein
Science V. 309 1377 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 12)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
1h: ADENOSINE-5'-DIPHOSPHATE (ADPh)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: FE(7)-MO-S(9)-N CLUSTER (CFNa)
3b: FE(7)-MO-S(9)-N CLUSTER (CFNb)
3c: FE(7)-MO-S(9)-N CLUSTER (CFNc)
3d: FE(7)-MO-S(9)-N CLUSTER (CFNd)
4a: FE(8)-S(7) CLUSTER (CLFa)
4b: FE(8)-S(7) CLUSTER (CLFb)
4c: FE(8)-S(7) CLUSTER (CLFc)
4d: FE(8)-S(7) CLUSTER (CLFd)
5a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
5b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
5c: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAc)
5d: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAd)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
6e: MAGNESIUM ION (MGe)
6f: MAGNESIUM ION (MGf)
6g: MAGNESIUM ION (MGg)
6h: MAGNESIUM ION (MGh)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
7d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
CFN
2
Ligand/Ion
FE(7)-MO-S(9)-N CLUSTER
4
CLF
2
Ligand/Ion
FE(8)-S(7) CLUSTER
5
HCA
2
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
6
MG
-1
Ligand/Ion
MAGNESIUM ION
7
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC7 (SOFTWARE)
02: AC8 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC1 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: CC7 (SOFTWARE)
08: CC8 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC2 (SOFTWARE)
12: DC3 (SOFTWARE)
13: DC4 (SOFTWARE)
14: DC5 (SOFTWARE)
15: DC6 (SOFTWARE)
16: DC7 (SOFTWARE)
17: DC8 (SOFTWARE)
18: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC7
SOFTWARE
ARG J:108 , GLU J:109 , HOH J:9004 , ASP L:353 , ASP L:357 , HOH L:9005
BINDING SITE FOR RESIDUE CA L 6492
02
AC8
SOFTWARE
ASP J:353 , ASP J:357 , HOH J:9007 , ARG L:108 , GLU L:109 , HOH L:9006
BINDING SITE FOR RESIDUE CA J 8492
03
AC9
SOFTWARE
SER M:16 , ADP M:5292
BINDING SITE FOR RESIDUE MG M 5291
04
BC1
SOFTWARE
ASP N:43 , ADP N:6292
BINDING SITE FOR RESIDUE MG N 6291
05
BC2
SOFTWARE
SER O:16 , ASP O:43 , ADP O:7292
BINDING SITE FOR RESIDUE MG O 7291
06
BC3
SOFTWARE
SER P:16 , ASP P:125 , ADP P:8292
BINDING SITE FOR RESIDUE MG P 8291
07
CC7
SOFTWARE
ALA I:65 , GLN I:191 , GLY I:424 , ILE I:425 , HIS I:442 , CFN I:496
BINDING SITE FOR RESIDUE HCA I 494
08
CC8
SOFTWARE
VAL I:70 , ARG I:96 , HIS I:195 , TYR I:229 , CYS I:275 , ILE I:355 , GLY I:357 , LEU I:358 , ARG I:359 , PHE I:381 , HIS I:442 , HCA I:494
BINDING SITE FOR RESIDUE CFN I 496
09
CC9
SOFTWARE
CYS I:62 , PRO I:85 , CYS I:88 , TYR I:91 , CYS I:154 , GLY I:185 , CYS J:70 , SER J:92 , GLY J:94 , CYS J:95 , TYR J:98 , CYS J:153 , SER J:188
BINDING SITE FOR RESIDUE CLF J 5498
10
DC1
SOFTWARE
ALA K:65 , GLN K:191 , GLY K:424 , ILE K:425 , HIS K:442 , CFN K:496
BINDING SITE FOR RESIDUE HCA K 494
11
DC2
SOFTWARE
VAL K:70 , ARG K:96 , HIS K:195 , TYR K:229 , CYS K:275 , ILE K:355 , GLY K:357 , LEU K:358 , ARG K:359 , PHE K:381 , HIS K:442 , HCA K:494
BINDING SITE FOR RESIDUE CFN K 496
12
DC3
SOFTWARE
CYS K:62 , PRO K:85 , CYS K:88 , TYR K:91 , CYS K:154 , GLY K:185 , CYS L:70 , SER L:92 , GLY L:94 , CYS L:95 , TYR L:98 , THR L:152 , CYS L:153 , SER L:188
BINDING SITE FOR RESIDUE CLF L 7498
13
DC4
SOFTWARE
CYS M:97 , ALA M:98 , CYS M:132 , CYS N:97 , CYS N:132
BINDING SITE FOR RESIDUE SF4 N 5290
14
DC5
SOFTWARE
GLY M:12 , GLY M:14 , LYS M:15 , SER M:16 , THR M:17 , ASN M:185 , VAL M:211 , PRO M:212 , ARG M:213 , ASP M:214 , TYR M:240 , MG M:5291
BINDING SITE FOR RESIDUE ADP M 5292
15
DC6
SOFTWARE
GLY N:12 , GLY N:14 , LYS N:15 , SER N:16 , THR N:17 , MG N:6291
BINDING SITE FOR RESIDUE ADP N 6292
16
DC7
SOFTWARE
CYS O:97 , ALA O:98 , CYS O:132 , CYS P:97 , ALA P:98 , CYS P:132 , GLY P:134 , PHE P:135
BINDING SITE FOR RESIDUE SF4 P 7290
17
DC8
SOFTWARE
LYS O:10 , GLY O:11 , GLY O:12 , ILE O:13 , GLY O:14 , LYS O:15 , SER O:16 , THR O:17 , ASP O:43 , ASN O:185 , ARG O:213 , ASP O:214 , TYR O:240 , MG O:7291
BINDING SITE FOR RESIDUE ADP O 7292
18
DC9
SOFTWARE
MET O:156 , GLY P:12 , ILE P:13 , GLY P:14 , LYS P:15 , SER P:16 , THR P:17 , PRO P:212 , ASP P:214 , MG P:8291
BINDING SITE FOR RESIDUE ADP P 8292
[
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]
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
(5, 17)
Info
All PROSITE Patterns/Profiles
1: NIFH_FRXC_3 (O:2-263)
2: NITROGENASE_1_1 (J:88-95,L:88-95)
3: NIFH_FRXC_1 (M:87-99,N:87-99,O:87-99,P:87-99)
4: NIFH_FRXC_2 (M:125-138,N:125-138,O:125-138,P:12...)
5: NITROGENASE_1_2 (J:151-165,L: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
1
-
-
-
-
O:2-263
2
NITROGENASE_1_1
PS00699
Nitrogenases component 1 alpha and beta subunits signature 1.
NIFD_AZOVI
81-88
2
-
-
I:81-88
K:81-88
NIFK_AZOVI
88-95
2
-
-
J:88-95
L:88-95
3
NIFH_FRXC_1
PS00746
NifH/frxC family signature 1.
NIFH1_AZOVI
88-100
4
-
-
-
-
M:87-99
N:87-99
O:87-99
P:87-99
4
NIFH_FRXC_2
PS00692
NifH/frxC family signature 2.
NIFH1_AZOVI
126-139
4
-
-
-
-
M:125-138
N:125-138
O:125-138
P:125-138
5
NITROGENASE_1_2
PS00090
Nitrogenases component 1 alpha and beta subunits signature 2.
NIFK_AZOVI
151-165
2
-
-
J:151-165
L:151-165
NIFD_AZOVI
152-166
2
-
-
I:152-166
K:152-166
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d2afia_ (A:)
1b: SCOP_d2afib_ (B:)
1c: SCOP_d2afic_ (C:)
1d: SCOP_d2afid_ (D:)
1e: SCOP_d2afii_ (I:)
1f: SCOP_d2afij_ (J:)
1g: SCOP_d2afik_ (K:)
1h: SCOP_d2afil_ (L:)
2a: SCOP_d2afie_ (E:)
2b: SCOP_d2afif_ (F:)
2c: SCOP_d2afig_ (G:)
2d: SCOP_d2afih_ (H:)
2e: SCOP_d2afim_ (M:)
2f: SCOP_d2afin_ (N:)
2g: SCOP_d2afio_ (O:)
2h: SCOP_d2afip_ (P:)
View:
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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
:
automated matches
(6)
Azotobacter vinelandii [TaxId: 354]
(6)
1a
d2afia_
A:
1b
d2afib_
B:
1c
d2afic_
C:
1d
d2afid_
D:
1e
d2afii_
I:
1f
d2afij_
J:
1g
d2afik_
K:
1h
d2afil_
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)
2a
d2afie_
E:
2b
d2afif_
F:
2c
d2afig_
G:
2d
d2afih_
H:
2e
d2afim_
M:
2f
d2afin_
N:
2g
d2afio_
O:
2h
d2afip_
P:
[
close SCOP info
]
CATH Domains
(3, 36)
Info
all CATH domains
1a: CATH_2afiA02 (A:63-205)
1b: CATH_2afiB02 (B:216-320)
1c: CATH_2afiD02 (D:216-320)
1d: CATH_2afiJ02 (J:216-320)
1e: CATH_2afiL02 (L:216-320)
1f: CATH_2afiA01 (A:5-62,A:345-479)
1g: CATH_2afiC01 (C:5-62,C:345-479)
1h: CATH_2afiI01 (I:5-62,I:345-479)
1i: CATH_2afiK01 (K:5-62,K:345-479)
1j: CATH_2afiC02 (C:63-205)
1k: CATH_2afiI02 (I:63-205)
1l: CATH_2afiK02 (K:63-205)
1m: CATH_2afiB01 (B:70-215)
1n: CATH_2afiD01 (D:70-215)
1o: CATH_2afiJ01 (J:70-215)
1p: CATH_2afiL01 (L:70-215)
1q: CATH_2afiA03 (A:206-320)
1r: CATH_2afiC03 (C:206-320)
1s: CATH_2afiI03 (I:206-320)
1t: CATH_2afiK03 (K:206-320)
1u: CATH_2afiB04 (B:365-470)
1v: CATH_2afiD04 (D:365-470)
1w: CATH_2afiJ04 (J:365-470)
1x: CATH_2afiL04 (L:365-470)
2a: CATH_2afiO00 (O:2-263)
2b: CATH_2afiG00 (G:1-263)
2c: CATH_2afiP00 (P:6-272)
2d: CATH_2afiM00 (M:4-271)
2e: CATH_2afiH00 (H:2-270)
2f: CATH_2afiN00 (N:4-273)
2g: CATH_2afiE00 (E:1-271)
2h: CATH_2afiF00 (F:1-275)
3a: CATH_2afiB03 (B:321-364,B:485-523)
3b: CATH_2afiD03 (D:321-364,D:485-523)
3c: CATH_2afiJ03 (J:321-364,J:485-523)
3d: CATH_2afiL03 (L:321-364,L:485-523)
View:
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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
2afiA02
A:63-205
1b
2afiB02
B:216-320
1c
2afiD02
D:216-320
1d
2afiJ02
J:216-320
1e
2afiL02
L:216-320
1f
2afiA01
A:5-62,A:345-479
1g
2afiC01
C:5-62,C:345-479
1h
2afiI01
I:5-62,I:345-479
1i
2afiK01
K:5-62,K:345-479
1j
2afiC02
C:63-205
1k
2afiI02
I:63-205
1l
2afiK02
K:63-205
1m
2afiB01
B:70-215
1n
2afiD01
D:70-215
1o
2afiJ01
J:70-215
1p
2afiL01
L:70-215
1q
2afiA03
A:206-320
1r
2afiC03
C:206-320
1s
2afiI03
I:206-320
1t
2afiK03
K:206-320
1u
2afiB04
B:365-470
1v
2afiD04
D:365-470
1w
2afiJ04
J:365-470
1x
2afiL04
L:365-470
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
2a
2afiO00
O:2-263
2b
2afiG00
G:1-263
2c
2afiP00
P:6-272
2d
2afiM00
M:4-271
2e
2afiH00
H:2-270
2f
2afiN00
N:4-273
2g
2afiE00
E:1-271
2h
2afiF00
F:1-275
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
2afiB03
B:321-364,B:485-523
3b
2afiD03
D:321-364,D:485-523
3c
2afiJ03
J:321-364,J:485-523
3d
2afiL03
L:321-364,L:485-523
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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