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2NSY
Asym. Unit
Info
Asym.Unit (107 KB)
Biol.Unit 1 (101 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS IN COMPLEX WITH NAD-ADENYLATE
Authors
:
M. Rizzi, M. Bolognesi, A. Coda
Date
:
14 Jul 98 (Deposition) - 13 Jan 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Ligase, Amidotransferase, Nh3 Dependent, Atp Pyrophosphatase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Rizzi, M. Bolognesi, A. Coda
A Novel Deamido-Nad+-Binding Site Revealed By The Trapped Nad-Adenylate Intermediate In The Nad+ Synthetase Structure
Structure V. 6 1129 1998
(for further references see the
PDB file header
)
[
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]
Hetero Components
(5, 12)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5a: PYROPHOSPHATE 2- (POPa)
5b: PYROPHOSPHATE 2- (POPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
2
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
GOL
2
Ligand/Ion
GLYCEROL
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
POP
2
Ligand/Ion
PYROPHOSPHATE 2-
[
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:50 , GLU A:162 , AMP A:300 , HOH A:675 , POP A:863
BINDING SITE FOR RESIDUE MG A 304
02
AC2
SOFTWARE
THR A:208 , AMP A:300 , HOH A:676 , HOH A:677 , POP A:863
BINDING SITE FOR RESIDUE MG A 305
03
AC3
SOFTWARE
THR B:208 , AMP B:302 , HOH B:679 , HOH B:680 , POP B:862
BINDING SITE FOR RESIDUE MG B 306
04
AC4
SOFTWARE
ASP B:50 , GLU B:162 , AMP B:302 , HOH B:678 , POP B:862
BINDING SITE FOR RESIDUE MG B 307
05
AC5
SOFTWARE
LEU A:43 , GLY A:44 , ILE A:45 , SER A:46 , SER A:51 , ARG A:78 , LEU A:79 , GLN A:84 , ARG A:139 , THR A:157 , GLU A:162 , ASP A:173 , THR A:208 , ALA A:209 , NAD A:301 , MG A:304 , MG A:305 , HOH A:331 , HOH A:350 , HOH A:382 , HOH A:569 , HOH A:675 , HOH A:677 , POP A:863
BINDING SITE FOR RESIDUE AMP A 300
06
AC6
SOFTWARE
PHE A:129 , ASN A:133 , ARG A:137 , PHE A:167 , PHE A:168 , THR A:169 , LYS A:170 , ASP A:173 , ALA A:209 , LEU A:211 , GLU A:223 , HIS A:257 , LYS A:258 , AMP A:300 , HOH A:349 , HOH A:389 , HOH A:433 , HOH A:448 , HOH A:540 , HOH A:569 , HOH A:595 , HOH A:835 , TYR B:32 , THR B:36 , TYR B:144 , LEU B:153 , ASP B:177 , HOH B:347 , HOH B:468
BINDING SITE FOR RESIDUE NAD A 301
07
AC7
SOFTWARE
LEU B:43 , GLY B:44 , ILE B:45 , SER B:46 , SER B:51 , ARG B:78 , LEU B:79 , GLN B:84 , ARG B:139 , THR B:157 , GLU B:162 , ASP B:173 , THR B:208 , ALA B:209 , NAD B:303 , MG B:306 , MG B:307 , HOH B:339 , HOH B:403 , HOH B:486 , HOH B:544 , HOH B:586 , HOH B:678 , HOH B:680 , POP B:862
BINDING SITE FOR RESIDUE AMP B 302
08
AC8
SOFTWARE
TYR A:32 , THR A:36 , TYR A:144 , LEU A:153 , ASP A:177 , HOH A:424 , HOH A:585 , ASN B:133 , ARG B:137 , PHE B:167 , PHE B:168 , THR B:169 , LYS B:170 , ASP B:173 , ALA B:209 , LEU B:211 , GLU B:223 , HIS B:257 , LYS B:258 , AMP B:302 , HOH B:418 , HOH B:486 , HOH B:499 , HOH B:520 , HOH B:530 , HOH B:579 , HOH B:586 , HOH B:648 , HOH B:811 , HOH B:850
BINDING SITE FOR RESIDUE NAD B 303
09
AC9
SOFTWARE
SER B:46 , GLY B:48 , GLN B:49 , ASP B:50 , SER B:51 , GLU B:162 , LYS B:186 , PRO B:207 , THR B:208 , AMP B:302 , MG B:306 , MG B:307 , HOH B:359 , HOH B:486 , HOH B:678 , HOH B:679 , HOH B:680
BINDING SITE FOR RESIDUE POP B 862
10
BC1
SOFTWARE
SER A:46 , GLY A:48 , GLN A:49 , ASP A:50 , SER A:51 , GLU A:162 , LYS A:186 , PRO A:207 , THR A:208 , AMP A:300 , MG A:304 , MG A:305 , HOH A:311 , HOH A:349 , HOH A:675 , HOH A:676 , HOH A:677
BINDING SITE FOR RESIDUE POP A 863
11
BC2
SOFTWARE
ASP A:158 , ALA A:163 , PHE A:168 , LYS A:258 , ARG A:259 , HOH A:800 , HOH A:801 , PRO B:262
BINDING SITE FOR RESIDUE GOL A 308
12
BC3
SOFTWARE
PRO A:262 , GLY B:174 , LYS B:258 , HOH B:332 , HOH B:463 , HOH B:607 , HOH B:799
BINDING SITE FOR RESIDUE GOL B 309
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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All PROSITE Patterns/Profiles
;
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Exons
(0, 0)
Info
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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, 2)
Info
All SCOP Domains
1a: SCOP_d2nsya_ (A:)
1b: SCOP_d2nsyb_ (B:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Adenine nucleotide alpha hydrolase-like
(440)
Superfamily
:
Adenine nucleotide alpha hydrolases-like
(110)
Family
:
N-type ATP pyrophosphatases
(44)
Protein domain
:
NH3-dependent NAD+-synthetase
(12)
Bacillus subtilis [TaxId: 1423]
(7)
1a
d2nsya_
A:
1b
d2nsyb_
B:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2nsyA00 (A:1-271)
1b: CATH_2nsyB00 (B:1-271)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Bacillus subtilis. Organism_taxid: 1423.
(3)
1a
2nsyA00
A:1-271
1b
2nsyB00
B:1-271
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_NAD_synthase_2nsyB01 (B:21-262)
1b: PFAM_NAD_synthase_2nsyB02 (B:21-262)
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(
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(
)
(
)
Clan
:
HUP
(230)
Family
:
NAD_synthase
(14)
Bacillus subtilis
(3)
1a
NAD_synthase-2nsyB01
B:21-262
1b
NAD_synthase-2nsyB02
B:21-262
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]
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (107 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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