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1QH8
Asym. Unit
Info
Asym.Unit (382 KB)
Biol.Unit 1 (373 KB)
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(1)
Title
:
NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, AS-CRYSTALLIZED (MIXED OXIDATION) STATE
Authors
:
S. M. Mayer, D. M. Lawson, C. A. Gormal, S. M. Roe, B. E. Smith
Date
:
11 May 99 (Deposition) - 01 Nov 99 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Biological Nitrogen Fixation, Nitrogen Metabolism, Molybdoenzymes, Electron Transfer, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. M. Mayer, D. M. Lawson, C. A. Gormal, S. M. Roe, B. E. Smith
New Insights Into Structure-Function Relationships In Nitrogenase: A 1. 6 A Resolution X-Ray Crystallographic Study Of Klebsiella Pneumoniae Mofe-Protein.
J. Mol. Biol. V. 292 871 1999
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 32)
Info
All Hetero Components
1a: FE-MO-S CLUSTER (CFMa)
1b: FE-MO-S CLUSTER (CFMb)
3a: FE(8)-S(7) CLUSTER (CLFa)
3b: FE(8)-S(7) CLUSTER (CLFb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
4e: 1,2-ETHANEDIOL (EDOe)
4f: 1,2-ETHANEDIOL (EDOf)
4g: 1,2-ETHANEDIOL (EDOg)
4h: 1,2-ETHANEDIOL (EDOh)
4i: 1,2-ETHANEDIOL (EDOi)
4j: 1,2-ETHANEDIOL (EDOj)
4k: 1,2-ETHANEDIOL (EDOk)
4l: 1,2-ETHANEDIOL (EDOl)
4m: 1,2-ETHANEDIOL (EDOm)
4n: 1,2-ETHANEDIOL (EDOn)
4o: 1,2-ETHANEDIOL (EDOo)
4p: 1,2-ETHANEDIOL (EDOp)
4q: 1,2-ETHANEDIOL (EDOq)
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)
6e: MAGNESIUM ION (MGe)
6f: MAGNESIUM ION (MGf)
6g: MAGNESIUM ION (MGg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CFM
2
Ligand/Ion
FE-MO-S CLUSTER
2
CL
2
Ligand/Ion
CHLORIDE ION
3
CLF
2
Ligand/Ion
FE(8)-S(7) CLUSTER
4
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
5
HCA
2
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
6
MG
7
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN D:395 , TRP D:398 , HOH D:3102 , HOH D:3123
BINDING SITE FOR RESIDUE CL D 2901
02
AC2
SOFTWARE
ASN B:395 , TRP B:398 , HOH B:3097
BINDING SITE FOR RESIDUE CL B 2902
03
AC3
SOFTWARE
HOH A:3609 , HOH A:3610 , HOH A:3611 , HOH A:3612 , HOH B:3799 , HOH B:3800
BINDING SITE FOR RESIDUE MG A 3001
04
AC4
SOFTWARE
ASP B:349 , ASP B:353 , HOH B:3801 , LYS D:106 , GLU D:107 , HOH D:3825
BINDING SITE FOR RESIDUE MG B 3002
05
AC5
SOFTWARE
HOH B:3802 , HOH B:3803 , HOH B:3804 , HOH B:3805 , HOH B:3806
BINDING SITE FOR RESIDUE MG B 3003
06
AC6
SOFTWARE
ASP B:407 , HOH B:3807 , HOH B:3808 , HOH B:3809 , HOH B:3810 , HOH B:3811
BINDING SITE FOR RESIDUE MG B 3004
07
AC7
SOFTWARE
HOH C:3026 , HOH C:3028 , HOH C:3029 , HOH C:3030 , HOH D:3826 , HOH D:3827
BINDING SITE FOR RESIDUE MG C 3005
08
AC8
SOFTWARE
LYS B:106 , GLU B:107 , HOH B:3812 , ASP D:349 , ASP D:353 , HOH D:3828
BINDING SITE FOR RESIDUE MG D 3006
09
AC9
SOFTWARE
HOH B:3813 , HOH B:3814 , GLN D:434 , HOH D:3829 , HOH D:3830 , HOH D:3831
BINDING SITE FOR RESIDUE MG D 3007
10
BC1
SOFTWARE
ALA A:64 , ARG A:95 , GLN A:190 , GLY A:422 , ILE A:423 , HIS A:440 , CFM A:503 , HOH A:3004 , HOH A:3006 , HOH A:3012 , HOH A:3030 , HOH A:3037 , HOH A:3592 , HOH A:3593 , HOH A:3594 , HOH A:3595 , HOH B:3037
BINDING SITE FOR RESIDUE HCA A 501
11
BC2
SOFTWARE
VAL A:69 , ARG A:95 , HIS A:194 , TYR A:227 , CYS A:273 , GLY A:354 , GLY A:355 , LEU A:356 , ARG A:357 , PHE A:379 , HIS A:440 , HCA A:501
BINDING SITE FOR RESIDUE CFM A 503
12
BC3
SOFTWARE
CYS A:61 , TYR A:63 , PRO A:84 , GLY A:86 , CYS A:87 , TYR A:90 , CYS A:153 , GLY A:184 , CYS B:68 , SER B:90 , GLY B:92 , CYS B:93 , TYR B:96 , CYS B:151 , SER B:186
BINDING SITE FOR RESIDUE CLF A 505
13
BC4
SOFTWARE
ALA C:64 , ARG C:95 , GLN C:190 , GLY C:422 , ILE C:423 , HIS C:440 , CFM C:503 , HOH C:1417 , HOH C:1419 , HOH C:1431 , HOH C:1434 , HOH C:1436 , HOH C:2032 , HOH C:2033 , HOH C:2039 , HOH C:2068 , HOH C:2078
BINDING SITE FOR RESIDUE HCA C 501
14
BC5
SOFTWARE
VAL C:69 , ARG C:95 , HIS C:194 , TYR C:227 , CYS C:273 , GLY C:354 , GLY C:355 , LEU C:356 , ARG C:357 , PHE C:379 , HIS C:440 , HCA C:501
BINDING SITE FOR RESIDUE CFM C 503
15
BC6
SOFTWARE
CYS C:61 , TYR C:63 , PRO C:84 , GLY C:86 , CYS C:87 , TYR C:90 , CYS C:153 , GLY C:184 , CYS D:68 , SER D:90 , CYS D:93 , TYR D:96 , CYS D:151 , SER D:186
BINDING SITE FOR RESIDUE CLF C 505
16
BC7
SOFTWARE
LYS B:237 , SER B:248 , LEU B:249 , ASP B:252 , GLU B:276 , HOH B:3440 , HOH B:3555
BINDING SITE FOR RESIDUE EDO B 2903
17
BC8
SOFTWARE
LEU B:501 , SER B:514 , ARG B:519 , HOH B:3702 , HOH B:3787 , TYR C:444 , SER D:9 , CYS D:10
BINDING SITE FOR RESIDUE EDO B 2904
18
BC9
SOFTWARE
GLU B:51 , PHE B:55 , ARG B:433 , HOH B:3580
BINDING SITE FOR RESIDUE EDO B 2905
19
CC1
SOFTWARE
ASN B:54 , PHE B:55 , ARG B:57 , HIS B:425 , HOH B:3645
BINDING SITE FOR RESIDUE EDO B 2906
20
CC2
SOFTWARE
HIS B:474 , HOH B:3254 , HOH B:3312 , HOH B:3413 , HOH B:3786 , MET D:350 , THR D:491
BINDING SITE FOR RESIDUE EDO B 2907
21
CC3
SOFTWARE
ASP A:443 , THR D:356 , TRP D:357 , HOH D:3008 , HOH D:3009 , HOH D:3012
BINDING SITE FOR RESIDUE EDO D 2908
22
CC4
SOFTWARE
LYS A:75 , THR A:100 , ASP A:254 , HOH A:3602 , PHE B:23 , GLU B:30 , HOH B:3800
BINDING SITE FOR RESIDUE EDO A 2909
23
CC5
SOFTWARE
ALA A:93 , ARG A:95 , ASN A:97 , TYR A:98 , THR A:110 , HOH A:3105 , HOH A:3449 , HOH A:3451 , HOH D:3071
BINDING SITE FOR RESIDUE EDO A 2910
24
CC6
SOFTWARE
PRO A:176 , ARG A:209 , GLU A:261 , HOH A:3225 , GLN D:36 , HOH D:3341
BINDING SITE FOR RESIDUE EDO A 2911
25
CC7
SOFTWARE
LYS A:267 , GLN A:313 , PHE A:314 , HOH A:3244 , HOH A:3301 , HOH A:3545
BINDING SITE FOR RESIDUE EDO A 2912
26
CC8
SOFTWARE
THR B:356 , TRP B:357 , HOH B:3777 , HOH B:3779 , ASP C:443 , TYR C:444
BINDING SITE FOR RESIDUE EDO B 2913
27
CC9
SOFTWARE
PRO C:176 , ASN C:208 , ARG C:209 , GLU C:261 , HOH C:1573 , HOH C:1589
BINDING SITE FOR RESIDUE EDO C 2914
28
DC1
SOFTWARE
ASN A:48 , LEU A:192 , HIS A:195 , TYR A:279 , HOH A:3088 , HOH A:3241
BINDING SITE FOR RESIDUE EDO A 2915
29
DC2
SOFTWARE
LYS D:237 , SER D:248 , LEU D:249 , ASP D:252 , GLU D:276 , HOH D:3380 , HOH D:3699
BINDING SITE FOR RESIDUE EDO D 2916
30
DC3
SOFTWARE
TYR A:444 , SER B:9 , CYS B:10 , LEU D:501 , SER D:514 , ARG D:519 , HOH D:3012
BINDING SITE FOR RESIDUE EDO D 2917
31
DC4
SOFTWARE
HOH C:1845 , ASN D:54 , PHE D:55 , ARG D:57 , HIS D:425
BINDING SITE FOR RESIDUE EDO D 2918
32
DC5
SOFTWARE
ARG D:27 , GLN D:28 , GLU D:31 , ALA D:32 , HOH D:3351 , HOH D:3775
BINDING SITE FOR RESIDUE EDO D 2919
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: NITROGENASE_1_1 (A:80-87,C:80-87,B:86-93,D:86-93)
2: NITROGENASE_1_2 (B:149-163,D:149-163,A:151-165,C:15...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NITROGENASE_1_1
PS00699
Nitrogenases component 1 alpha and beta subunits signature 1.
NIFD_KLEPN
82-89
2
A:80-87
C:80-87
NIFK_KLEPN
87-94
2
B:86-93
D:86-93
2
NITROGENASE_1_2
PS00090
Nitrogenases component 1 alpha and beta subunits signature 2.
NIFK_KLEPN
150-164
2
B:149-163
D:149-163
NIFD_KLEPN
153-167
2
A:151-165
C:151-165
[
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1qh8a_ (A:)
1b: SCOP_d1qh8c_ (C:)
2a: SCOP_d1qh8b_ (B:)
2b: SCOP_d1qh8d_ (D:)
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Classes
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)
(
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)
(
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(
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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)
Klebsiella pneumoniae [TaxId: 573]
(4)
1a
d1qh8a_
A:
1b
d1qh8c_
C:
Protein domain
:
Nitrogenase iron-molybdenum protein, beta chain
(20)
Klebsiella pneumoniae [TaxId: 573]
(4)
2a
d1qh8b_
B:
2b
d1qh8d_
D:
[
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]
CATH Domains
(2, 14)
Info
all CATH domains
1a: CATH_1qh8A02 (A:62-204)
1b: CATH_1qh8B01 (B:68-211)
1c: CATH_1qh8D01 (D:68-211)
1d: CATH_1qh8A03 (A:205-318)
1e: CATH_1qh8C03 (C:205-318)
1f: CATH_1qh8B03 (B:361-466)
1g: CATH_1qh8D03 (D:361-466)
1h: CATH_1qh8B02 (B:212-316)
1i: CATH_1qh8D02 (D:212-316)
1j: CATH_1qh8A01 (A:1-61,A:343-477)
1k: CATH_1qh8C01 (C:1-61,C:343-477)
1l: CATH_1qh8C02 (C:62-204)
2a: CATH_1qh8B04 (B:317-360,B:481-519)
2b: CATH_1qh8D04 (D:317-360,D:481-519)
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Topologies
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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)
Klebsiella pneumoniae. Organism_taxid: 573. Strain: m5a1. Variant: wild-type.
(3)
1a
1qh8A02
A:62-204
1b
1qh8B01
B:68-211
1c
1qh8D01
D:68-211
1d
1qh8A03
A:205-318
1e
1qh8C03
C:205-318
1f
1qh8B03
B:361-466
1g
1qh8D03
D:361-466
1h
1qh8B02
B:212-316
1i
1qh8D02
D:212-316
1j
1qh8A01
A:1-61,A:343-477
1k
1qh8C01
C:1-61,C:343-477
1l
1qh8C02
C:62-204
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)
Klebsiella pneumoniae. Organism_taxid: 573. Strain: m5a1. Variant: wild-type.
(3)
2a
1qh8B04
B:317-360,B:481-519
2b
1qh8D04
D:317-360,D:481-519
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_DUF3364_1qh8D01 (D:1-54)
1b: PFAM_DUF3364_1qh8D02 (D:1-54)
2a: PFAM_Oxidored_nitro_1qh8C01 (C:61-466)
2b: PFAM_Oxidored_nitro_1qh8C02 (C:61-466)
2c: PFAM_Oxidored_nitro_1qh8D03 (D:68-498)
2d: PFAM_Oxidored_nitro_1qh8D04 (D:68-498)
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Clans
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)
(
)
Clan
:
no clan defined [family: DUF3364]
(10)
Family
:
DUF3364
(10)
Klebsiella pneumoniae
(2)
1a
DUF3364-1qh8D01
D:1-54
1b
DUF3364-1qh8D02
D:1-54
Clan
:
no clan defined [family: Oxidored_nitro]
(12)
Family
:
Oxidored_nitro
(12)
Klebsiella pneumoniae
(2)
2a
Oxidored_nitro-1qh8C01
C:61-466
2b
Oxidored_nitro-1qh8C02
C:61-466
2c
Oxidored_nitro-1qh8D03
D:68-498
2d
Oxidored_nitro-1qh8D04
D:68-498
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