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2AFH
Asym. Unit
Info
Asym.Unit (466 KB)
Biol.Unit 1 (455 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NUCLEOTIDE-FREE 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
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (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
)
[
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Hetero Components
(12, 28)
Info
All Hetero Components
01a: PENTAETHYLENE GLYCOL (1PEa)
01b: PENTAETHYLENE GLYCOL (1PEb)
02a: CALCIUM ION (CAa)
02b: CALCIUM ION (CAb)
03a: FE(7)-MO-S(9)-N CLUSTER (CFNa)
03b: FE(7)-MO-S(9)-N CLUSTER (CFNb)
04a: FE(8)-S(7) CLUSTER (CLFa)
04b: FE(8)-S(7) CLUSTER (CLFb)
05a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
05b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
06a: SODIUM ION (NAa)
07a: HEXAETHYLENE GLYCOL (P6Ga)
08a: DI(HYDROXYETHYL)ETHER (PEGa)
08b: DI(HYDROXYETHYL)ETHER (PEGb)
08c: DI(HYDROXYETHYL)ETHER (PEGc)
09a: TETRAETHYLENE GLYCOL (PG4a)
09b: TETRAETHYLENE GLYCOL (PG4b)
10a: TRIETHYLENE GLYCOL (PGEa)
10b: TRIETHYLENE GLYCOL (PGEb)
10c: TRIETHYLENE GLYCOL (PGEc)
10d: TRIETHYLENE GLYCOL (PGEd)
10e: TRIETHYLENE GLYCOL (PGEe)
10f: TRIETHYLENE GLYCOL (PGEf)
10g: TRIETHYLENE GLYCOL (PGEg)
10h: TRIETHYLENE GLYCOL (PGEh)
11a: IRON/SULFUR CLUSTER (SF4a)
12a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
12b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
CA
2
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
NA
1
Ligand/Ion
SODIUM ION
7
P6G
1
Ligand/Ion
HEXAETHYLENE GLYCOL
8
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
9
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
10
PGE
8
Ligand/Ion
TRIETHYLENE GLYCOL
11
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
12
TRS
2
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(28, 28)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:108 , GLU B:109 , HOH B:5021 , ASP D:353 , ASP D:357 , HOH D:5022
BINDING SITE FOR RESIDUE CA D 2490
02
AC2
SOFTWARE
ASP B:353 , ASP B:357 , HOH B:5022 , ARG D:108 , GLU D:109 , HOH D:5023
BINDING SITE FOR RESIDUE CA B 2491
03
AC3
SOFTWARE
HOH A:5370 , HOH B:5612 , HOH B:5613 , HOH B:5614
BINDING SITE FOR RESIDUE NA B 2492
04
AC4
SOFTWARE
ALA A:65 , GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , CFN A:2496 , HOH A:5038 , HOH A:5049 , HOH A:5071 , HOH A:5084 , HOH A:5094 , HOH A:5264 , HOH A:5267 , HOH B:5431 , HOH B:5465 , HOH B:5482
BINDING SITE FOR RESIDUE HCA A 2494
05
AC5
SOFTWARE
VAL A:70 , ARG A:96 , HIS A:195 , TYR A:229 , CYS A:275 , SER A:278 , GLY A:356 , GLY A:357 , LEU A:358 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:2494
BINDING SITE FOR RESIDUE CFN A 2496
06
AC6
SOFTWARE
CYS A:62 , TYR A:64 , PRO A:85 , GLY A:87 , CYS A:88 , TYR A:91 , CYS A:154 , GLY A:185 , CYS B:70 , SER B:92 , CYS B:95 , TYR B:98 , CYS B:153 , SER B:188
BINDING SITE FOR RESIDUE CLF B 2498
07
AC7
SOFTWARE
ALA C:65 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , CFN C:3496 , HOH C:5030 , HOH C:5045 , HOH C:5059 , HOH C:5063 , HOH C:5064 , HOH C:5067 , HOH C:5203 , HOH C:5209 , HOH C:5278 , HOH D:5138
BINDING SITE FOR RESIDUE HCA C 3494
08
AC8
SOFTWARE
VAL C:70 , ARG C:96 , HIS C:195 , TYR C:229 , CYS C:275 , 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 CFN C 3496
09
AC9
SOFTWARE
CYS C:62 , TYR C:64 , PRO C:85 , GLY C:87 , CYS C:88 , TYR C:91 , CYS C:154 , GLY C:185 , CYS D:70 , SER D:92 , CYS D:95 , TYR D:98 , CYS D:153 , SER D:188
BINDING SITE FOR RESIDUE CLF C 3498
10
BC1
SOFTWARE
CYS E:97 , ALA E:98 , CYS E:132 , GLY E:134 , CYS F:97 , ALA F:98 , CYS F:132 , GLY F:134
BINDING SITE FOR RESIDUE SF4 E 3290
11
BC2
SOFTWARE
MET B:213 , LYS B:216 , VAL B:218 , LYS B:310 , HOH B:5063 , HOH B:5155 , HOH B:5425 , HOH B:5495 , HOH B:5590
BINDING SITE FOR RESIDUE TRS B 5003
12
BC3
SOFTWARE
GLU C:287 , PRO C:293 , TRP C:294
BINDING SITE FOR RESIDUE TRS C 5004
13
BC4
SOFTWARE
PRO B:295 , TRP B:296 , GLU B:299 , LYS B:315 , ASN B:317 , HOH B:5225
BINDING SITE FOR RESIDUE PGE B 5005
14
BC5
SOFTWARE
PRO D:295 , TRP D:296 , LYS D:315 , LEU D:316 , HOH D:5383 , HOH D:5478
BINDING SITE FOR RESIDUE PGE D 5006
15
BC6
SOFTWARE
MET E:29 , GLY E:30 , LYS E:31 , ASP E:120 , VAL E:248 , HOH E:5101
BINDING SITE FOR RESIDUE PG4 E 5007
16
BC7
SOFTWARE
GLU D:33 , LYS D:34 , TYR D:35 , HOH D:5535
BINDING SITE FOR RESIDUE PGE D 5008
17
BC8
SOFTWARE
GLN D:53 , GLY D:307 , LYS D:310 , HIS D:311 , GLU D:312 , VAL D:421 , TYR D:422 , ILE D:423 , HOH D:5223 , HOH D:5316
BINDING SITE FOR RESIDUE P6G D 5009
18
BC9
SOFTWARE
PHE D:183 , TYR D:207
BINDING SITE FOR RESIDUE PGE D 5010
19
CC1
SOFTWARE
LEU C:467 , ASN C:468 , TRP C:472 , LYS C:473 , HOH C:5340
BINDING SITE FOR RESIDUE PGE C 5011
20
CC2
SOFTWARE
ASP A:204 , TRP A:205 , HOH A:5161
BINDING SITE FOR RESIDUE PGE A 5012
21
CC3
SOFTWARE
HIS B:363 , GLU B:389 , PRO B:414 , TYR B:415 , LYS B:417 , ARG C:345 , ASP C:464 , ASN C:468 , HOH C:5305 , HOH C:5310 , HOH C:5344
BINDING SITE FOR RESIDUE 1PE C 5013
22
CC4
SOFTWARE
GLU B:299 , LYS B:300 , LYS B:303 , ARG B:401 , HOH B:5282 , HOH B:5394 , GLU F:110 , TYR F:115 , HOH F:352
BINDING SITE FOR RESIDUE PG4 B 5014
23
CC5
SOFTWARE
THR A:303 , ILE A:306 , GLU A:307 , TRP A:335 , HOH A:5155 , HOH A:5340
BINDING SITE FOR RESIDUE PGE A 5015
24
CC6
SOFTWARE
THR C:303 , ILE C:306 , TRP C:335 , ASP C:369 , HOH C:5090 , HOH C:5121
BINDING SITE FOR RESIDUE PGE C 5016
25
CC7
SOFTWARE
THR B:48 , THR B:49 , PHE B:435 , THR B:436 , ASP B:437 , LYS B:438 , LYS B:458 , GLU B:461 , PHE B:462 , HOH B:5061 , HOH B:5080 , HOH B:5124 , HOH B:5177 , GLU E:287 , GLU E:288 , HOH E:5121
BINDING SITE FOR RESIDUE 1PE B 5017
26
CC8
SOFTWARE
PHE B:57 , TYR B:422 , HOH B:5289
BINDING SITE FOR RESIDUE PEG B 5018
27
CC9
SOFTWARE
GLU D:42 , TRP D:46 , LYS D:222
BINDING SITE FOR RESIDUE PEG D 5019
28
DC1
SOFTWARE
PRO A:470 , LYS D:381 , LEU D:384 , GLU D:385 , SER D:413 , HOH D:5183 , HOH D:5200
BINDING SITE FOR RESIDUE PEG D 5020
[
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, 14)
Info
All PROSITE Patterns/Profiles
1: NIFH_FRXC_3 (E:2-274,F:2-274)
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)
4: NIFH_FRXC_2 (E:125-138,F:125-138)
5: NITROGENASE_1_2 (B:151-165,D:151-165,A:152-166,C:15...)
;
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
2
E:2-274
F: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
2
E:87-99
F:87-99
4
NIFH_FRXC_2
PS00692
NifH/frxC family signature 2.
NIFH1_AZOVI
126-139
2
E:125-138
F: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
View:
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All Exon Boundaries
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2afha_ (A:)
1b: SCOP_d2afhc_ (C:)
2a: SCOP_d2afhb_ (B:)
2b: SCOP_d2afhd_ (D:)
3a: SCOP_d2afhe_ (E:)
3b: SCOP_d2afhf_ (F:)
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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
d2afha_
A:
1b
d2afhc_
C:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Azotobacter vinelandii [TaxId: 354]
(15)
2a
d2afhb_
B:
2b
d2afhd_
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
d2afhe_
E:
3b
d2afhf_
F:
[
close SCOP info
]
CATH Domains
(3, 16)
Info
all CATH domains
1a: CATH_2afhA02 (A:63-205)
1b: CATH_2afhC02 (C:63-205)
1c: CATH_2afhA01 (A:5-62,A:345-479)
1d: CATH_2afhC01 (C:4-62,C:345-479)
1e: CATH_2afhB01 (B:70-215)
1f: CATH_2afhD01 (D:70-215)
1g: CATH_2afhA03 (A:206-320)
1h: CATH_2afhC03 (C:206-320)
1i: CATH_2afhB04 (B:365-470)
1j: CATH_2afhD04 (D:365-470)
1k: CATH_2afhB02 (B:216-320)
1l: CATH_2afhD02 (D:216-320)
2a: CATH_2afhF00 (F:1-286)
2b: CATH_2afhE00 (E:1-289)
3a: CATH_2afhB03 (B:321-364,B:485-523)
3b: CATH_2afhD03 (D:321-364,D:485-523)
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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
2afhA02
A:63-205
1b
2afhC02
C:63-205
1c
2afhA01
A:5-62,A:345-479
1d
2afhC01
C:4-62,C:345-479
1e
2afhB01
B:70-215
1f
2afhD01
D:70-215
1g
2afhA03
A:206-320
1h
2afhC03
C:206-320
1i
2afhB04
B:365-470
1j
2afhD04
D:365-470
1k
2afhB02
B:216-320
1l
2afhD02
D:216-320
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
2a
2afhF00
F:1-286
2b
2afhE00
E: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
2afhB03
B:321-364,B:485-523
3b
2afhD03
D:321-364,D:485-523
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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