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2NU6
Asym. Unit
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
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:243 , HOH A:1528 , MET B:1 , GLY B:220 , ARG B:233
BINDING SITE FOR RESIDUE SO4 A 1500
02
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
03
AC3
SOFTWARE
GLY E:52 , GLY E:53 , ARG E:54 , GLY E:55 , ASP E:213 , HOH E:1521
BINDING SITE FOR RESIDUE SO4 E 1401
04
AC4
SOFTWARE
ARG D:243 , MET E:1 , GLY E:220 , ARG E:233 , HOH E:1550
BINDING SITE FOR RESIDUE SO4 E 1501
05
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
06
AC6
SOFTWARE
TYR B:23 , ALA B:24 , CYS B:25 , GLU B:30 , LYS B:37
BINDING SITE FOR RESIDUE COA B 1025
07
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
08
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
09
AC9
SOFTWARE
TYR E:23 , ALA E:24 , CYS E:25 , GLU E:30 , LYS E:37
BINDING SITE FOR RESIDUE COA E 1025
10
BC1
SOFTWARE
GLY E:320 , GLY E:321 , ILE E:322 , VAL E:323 , CYS E:325 , ILE E:328 , GLU E:350 , ASN E:352
BINDING SITE FOR RESIDUE COA E 1325
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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,D:151-180)
2: SUCCINYL_COA_LIG_2 (A:235-248,D:235-248)
3: SUCCINYL_COA_LIG_3 (B:257-282,E: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
D: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
D: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
E:257-282
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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)
(
)
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)
(
)
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
[
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]
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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(
)
(
)
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(
)
(
)
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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