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2NU6
Biol. Unit 1
Info
Asym.Unit (217 KB)
Biol.Unit 1 (210 KB)
Biol.Unit 2 (210 KB)
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(1)
Title
:
C123AA MUTANT OF E. COLI SUCCINYL-COA SYNTHETASE
Authors
:
M. E. Fraser
Date
:
08 Nov 06 (Deposition) - 24 Jul 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B (2x)
Biol. Unit 2: D,E (2x)
Keywords
:
Citric Acid Cycle, Heterotetramer, Ligase, Atp-Grasp Fold, Rossmann Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Hidber, E. R. Brownie, K. Hayakawa, M. E. Fraser
Participation Of Cys 123Alpha Of Escherichia Coli Succinyl-Coa Synthetase In Catalysis
Acta Crystallogr. , Sect. D V. 63 876 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: COENZYME A (COAa)
1b: COENZYME A (COAb)
1c: COENZYME A (COAc)
1d: COENZYME A (COAd)
1e: COENZYME A (COAe)
1f: COENZYME A (COAf)
2a: N1-PHOSPHONOHISTIDINE (NEPa)
2b: N1-PHOSPHONOHISTIDINE (NEPb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
6
Ligand/Ion
COENZYME A
2
NEP
2
Mod. Amino Acid
N1-PHOSPHONOHISTIDINE
3
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:243 , HOH A:1528 , MET B:1 , GLY B:220 , ARG B:233
BINDING SITE FOR RESIDUE SO4 A 1500
2
AC2
SOFTWARE
GLY B:52 , GLY B:53 , ARG B:54 , GLY B:55 , ASP B:213 , HOH B:1456
BINDING SITE FOR RESIDUE SO4 B 1400
3
AC5
SOFTWARE
GLY A:14 , THR A:16 , GLY A:17 , SER A:18 , GLN A:19 , VAL A:38 , THR A:39 , PRO A:40 , LYS A:42 , TYR A:71 , VAL A:72 , PRO A:73 , SER A:80 , ILE A:95 , THR A:96 , GLU A:97 , ASN A:122 , ALA A:123 , PRO A:124 , ILE A:136 , NEP A:246 , HOH A:1503 , HOH A:1504 , HOH A:1505 , HOH A:1541 , HOH A:1565 , ARG B:161 , ARG E:29 , GLU E:33 , SER E:36 , LYS E:66
BINDING SITE FOR RESIDUE COA A 1300
4
AC6
SOFTWARE
TYR B:23 , ALA B:24 , CYS B:25 , GLU B:30 , LYS B:37
BINDING SITE FOR RESIDUE COA B 1025
5
AC7
SOFTWARE
GLY B:320 , GLY B:321 , ILE B:322 , VAL B:323 , CYS B:325 , GLU B:350 , ASN B:352
BINDING SITE FOR RESIDUE COA B 1325
6
AC8
SOFTWARE
ARG B:29 , GLU B:33 , SER B:36 , LYS B:66 , GLY D:14 , THR D:16 , GLY D:17 , SER D:18 , GLN D:19 , VAL D:38 , THR D:39 , PRO D:40 , LYS D:42 , TYR D:71 , VAL D:72 , PRO D:73 , ASP D:79 , SER D:80 , ILE D:95 , THR D:96 , GLU D:97 , ASN D:122 , ALA D:123 , PRO D:124 , ILE D:136 , HOH D:1309 , HOH D:1320 , HOH D:1330 , ARG E:161
BINDING SITE FOR RESIDUE COA D 1301
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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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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: SUCCINYL_COA_LIG_1 (A:151-180)
2: SUCCINYL_COA_LIG_2 (A:235-248)
3: SUCCINYL_COA_LIG_3 (B:257-282)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUCCINYL_COA_LIG_1
PS01216
ATP-citrate lyase / succinyl-CoA ligases family signature 1.
SUCD_ECOLI
152-181
2
A:151-180
-
2
SUCCINYL_COA_LIG_2
PS00399
ATP-citrate lyase / succinyl-CoA ligases family active site.
SUCD_ECOLI
236-249
2
A:235-248
-
3
SUCCINYL_COA_LIG_3
PS01217
ATP-citrate lyase / succinyl-CoA ligases family signature 3.
SUCC_ECOLI
257-282
2
B:257-282
-
[
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]
Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d2nu6b2 (B:1-238)
1b: SCOP_d2nu6e2 (E:1-238)
2a: SCOP_d2nu6a2 (A:122-287)
2b: SCOP_d2nu6d2 (D:122-287)
3a: SCOP_d2nu6b1 (B:239-388)
3b: SCOP_d2nu6e1 (E:239-385)
4a: SCOP_d2nu6a1 (A:1-121)
4b: SCOP_d2nu6d1 (D:1-121)
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Classes
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)
(
)
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)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
Succinyl-CoA synthetase, beta-chain, N-terminal domain
(17)
Protein domain
:
Succinyl-CoA synthetase, beta-chain, N-terminal domain
(17)
Escherichia coli [TaxId: 562]
(11)
1a
d2nu6b2
B:1-238
1b
d2nu6e2
E:1-238
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Succinyl-CoA synthetase domains
(39)
Family
:
Succinyl-CoA synthetase domains
(38)
Protein domain
:
Succinyl-CoA synthetase, alpha-chain, C-terminal domain
(20)
Escherichia coli [TaxId: 562]
(11)
2a
d2nu6a2
A:122-287
2b
d2nu6d2
D:122-287
Protein domain
:
Succinyl-CoA synthetase, beta-chain, C-terminal domain
(17)
Escherichia coli [TaxId: 562]
(11)
3a
d2nu6b1
B:239-388
3b
d2nu6e1
E:239-385
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
CoA-binding domain
(29)
Protein domain
:
Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain
(20)
Escherichia coli [TaxId: 562]
(11)
4a
d2nu6a1
A:1-121
4b
d2nu6d1
D:1-121
[
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]
CATH Domains
(4, 10)
Info
all CATH domains
1a: CATH_2nu6B01 (B:1-20,B:105-239)
1b: CATH_2nu6E01 (E:1-20,E:105-239)
2a: CATH_2nu6B02 (B:21-104)
2b: CATH_2nu6E02 (E:21-104)
3a: CATH_2nu6A02 (A:123-287)
3b: CATH_2nu6B03 (B:240-388)
3c: CATH_2nu6E03 (E:240-385)
3d: CATH_2nu6D02 (D:123-287)
4a: CATH_2nu6A01 (A:1-122)
4b: CATH_2nu6D01 (D:1-122)
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)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
ATP-grasp fold, B domain
(118)
Escherichia coli. Organism_taxid: 562.
(17)
1a
2nu6B01
B:1-20,B:105-239
1b
2nu6E01
E:1-20,E:105-239
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Escherichia coli. Organism_taxid: 562.
(15)
2a
2nu6B02
B:21-104
2b
2nu6E02
E:21-104
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.261, no name defined]
(20)
Escherichia coli. Organism_taxid: 562.
(5)
3a
2nu6A02
A:123-287
3b
2nu6B03
B:240-388
3c
2nu6E03
E:240-385
3d
2nu6D02
D:123-287
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562.
(48)
4a
2nu6A01
A:1-122
4b
2nu6D01
D:1-122
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_ATP_grasp_2_2nu6E01 (E:2-203)
1b: PFAM_ATP_grasp_2_2nu6E02 (E:2-203)
2a: PFAM_CoA_binding_2nu6D01 (D:5-98)
2b: PFAM_CoA_binding_2nu6D02 (D:5-98)
3a: PFAM_Ligase_CoA_2nu6E03 (E:262-382)
3b: PFAM_Ligase_CoA_2nu6E04 (E:262-382)
3c: PFAM_Ligase_CoA_2nu6D03 (D:150-271)
3d: PFAM_Ligase_CoA_2nu6D04 (D:150-271)
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Clans
(
)
(
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(
)
(
)
Organisms
(
)
(
)
Clan
:
ATP-grasp
(83)
Family
:
ATP-grasp_2
(10)
Escherichia coli (strain K12)
(8)
1a
ATP-grasp_2-2nu6E01
E:2-203
1b
ATP-grasp_2-2nu6E02
E:2-203
Clan
:
NADP_Rossmann
(1239)
Family
:
CoA_binding
(18)
Escherichia coli (strain K12)
(6)
2a
CoA_binding-2nu6D01
D:5-98
2b
CoA_binding-2nu6D02
D:5-98
Clan
:
Succ_CoA_synth
(13)
Family
:
Ligase_CoA
(13)
Escherichia coli (strain K12)
(8)
3a
Ligase_CoA-2nu6E03
E:262-382
3b
Ligase_CoA-2nu6E04
E:262-382
3c
Ligase_CoA-2nu6D03
D:150-271
3d
Ligase_CoA-2nu6D04
D:150-271
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