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2IHV
Asym. Unit
Info
Asym.Unit (367 KB)
Biol.Unit 1 (359 KB)
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(1)
Title
:
CARBOXYETHYLARGININE SYNTHASE FROM STREPTOMYCES CLAVULIGERUS: 5-GUANIDINOVALERIC ACID COMPLEX
Authors
:
M. E. Caines, C. J. Schofield
Date
:
27 Sep 06 (Deposition) - 18 Sep 07 (Release) - 17 Nov 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Thiamin Diphosphate Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. E. Caines, J. L. Sorensen, C. J. Schofield
Structural And Mechanistic Studies On N(2)-(2-Carboxyethyl)Arginine Synthase.
Biochem. Biophys. Res. Commun. V. 385 512 2009
(for further references see the
PDB file header
)
[
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]
Hetero Components
(4, 18)
Info
All Hetero Components
1a: 5-{[AMINO(IMINO)METHYL]AMINO}PENTA... (GVAa)
1b: 5-{[AMINO(IMINO)METHYL]AMINO}PENTA... (GVAb)
1c: 5-{[AMINO(IMINO)METHYL]AMINO}PENTA... (GVAc)
1d: 5-{[AMINO(IMINO)METHYL]AMINO}PENTA... (GVAd)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
2e: POTASSIUM ION (Ke)
2f: POTASSIUM ION (Kf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: THIAMINE DIPHOSPHATE (TPPa)
4b: THIAMINE DIPHOSPHATE (TPPb)
4c: THIAMINE DIPHOSPHATE (TPPc)
4d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GVA
4
Ligand/Ion
5-{[AMINO(IMINO)METHYL]AMINO}PENTANOIC ACID
2
K
6
Ligand/Ion
POTASSIUM ION
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:463 , ASN A:490 , THR A:492 , TPP A:600 , HOH A:662
BINDING SITE FOR RESIDUE MG A 601
02
AC2
SOFTWARE
GLU A:396 , GLU A:397 , ALA A:399
BINDING SITE FOR RESIDUE K A 602
03
AC3
SOFTWARE
ASP B:463 , ASN B:490 , THR B:492 , TPP B:600 , HOH B:1068
BINDING SITE FOR RESIDUE MG B 601
04
AC4
SOFTWARE
GLU B:396 , GLU B:397 , ALA B:399
BINDING SITE FOR RESIDUE K B 602
05
AC5
SOFTWARE
HIS A:56 , SER A:468 , HOH A:672 , HOH A:766 , HIS B:56 , SER B:468 , HOH B:1016 , HOH B:1119
BINDING SITE FOR RESIDUE K B 995
06
AC6
SOFTWARE
ASP C:463 , ASN C:490 , THR C:492 , TPP C:600 , HOH C:1108
BINDING SITE FOR RESIDUE MG C 601
07
AC7
SOFTWARE
GLU C:396 , GLU C:397 , ALA C:399
BINDING SITE FOR RESIDUE K C 602
08
AC8
SOFTWARE
HIS C:56 , SER C:468 , HOH C:1035 , HOH C:1135 , HIS D:56 , SER D:468 , HOH D:667 , HOH D:758
BINDING SITE FOR RESIDUE K C 996
09
AC9
SOFTWARE
ASP D:463 , ASN D:490 , THR D:492 , TPP D:600 , HOH D:739
BINDING SITE FOR RESIDUE MG D 601
10
BC1
SOFTWARE
GLU D:396 , GLU D:397 , ALA D:399
BINDING SITE FOR RESIDUE K D 602
11
BC2
SOFTWARE
ILE A:410 , GLY A:411 , PHE A:412 , PHE A:413 , SER A:436 , SER A:437 , PHE A:438 , GLY A:462 , ASP A:463 , GLY A:464 , GLY A:465 , ASN A:490 , THR A:492 , ASN A:493 , GLY A:494 , LEU A:495 , TYR A:561 , MG A:601 , HOH A:658 , GLU B:57 , THR B:80 , PRO B:83 , ASN B:87
BINDING SITE FOR RESIDUE TPP A 600
12
BC3
SOFTWARE
TYR A:271 , ASP A:301 , ARG A:303 , MET A:306 , ARG A:414 , HIS A:415 , LEU A:571 , ILE A:573 , HOH A:641 , HOH A:667 , HOH A:694 , GLN B:121
BINDING SITE FOR RESIDUE GVA A 603
13
BC4
SOFTWARE
GLU A:57 , THR A:80 , PRO A:83 , ASN A:87 , ILE B:410 , GLY B:411 , PHE B:412 , PHE B:413 , SER B:436 , SER B:437 , PHE B:438 , GLY B:462 , ASP B:463 , GLY B:464 , GLY B:465 , ASN B:490 , THR B:492 , ASN B:493 , GLY B:494 , LEU B:495 , TYR B:561 , MG B:601 , HOH B:1000
BINDING SITE FOR RESIDUE TPP B 600
14
BC5
SOFTWARE
HIS A:120 , TYR B:271 , ASP B:301 , ARG B:303 , ARG B:414 , HIS B:415 , LEU B:495 , LEU B:571 , ILE B:573 , HOH B:1103 , HOH B:1106 , HOH B:1116
BINDING SITE FOR RESIDUE GVA B 603
15
BC6
SOFTWARE
ILE C:410 , GLY C:411 , PHE C:412 , PHE C:413 , SER C:436 , SER C:437 , PHE C:438 , GLY C:462 , ASP C:463 , GLY C:464 , GLY C:465 , ASN C:490 , THR C:492 , ASN C:493 , GLY C:494 , LEU C:495 , TYR C:561 , MG C:601 , HOH C:1049 , GLU D:57 , THR D:80 , ASN D:87
BINDING SITE FOR RESIDUE TPP C 600
16
BC7
SOFTWARE
TYR C:271 , ASP C:301 , ARG C:303 , ARG C:414 , HIS C:415 , SER C:436 , TYR C:499 , HOH C:1226 , HOH C:1228 , HOH C:1229 , HIS D:120
BINDING SITE FOR RESIDUE GVA C 603
17
BC8
SOFTWARE
GLU C:57 , THR C:80 , PRO C:83 , ASN C:87 , ILE D:410 , GLY D:411 , PHE D:412 , PHE D:413 , SER D:436 , SER D:437 , PHE D:438 , GLY D:462 , ASP D:463 , GLY D:464 , GLY D:465 , ASN D:490 , THR D:492 , ASN D:493 , GLY D:494 , LEU D:495 , TYR D:561 , MG D:601 , HOH D:604 , HOH D:739
BINDING SITE FOR RESIDUE TPP D 600
18
BC9
SOFTWARE
HIS C:120 , GLN C:121 , TYR D:271 , ASP D:301 , ARG D:303 , MET D:306 , ILE D:410 , ARG D:414 , HIS D:415 , LEU D:571 , ILE D:573 , HOH D:629 , HOH D:681 , HOH D:700
BINDING SITE FOR RESIDUE GVA D 603
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (A:446-465,B:446-465,C:446-465,D:44...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
CEAS_STRCL
446-465
4
A:446-465
B:446-465
C:446-465
D:446-465
[
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Exons
(0, 0)
Info
All Exons
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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, 12)
Info
All SCOP Domains
1a: SCOP_d2ihva1 (A:198-374)
1b: SCOP_d2ihvc2 (C:198-374)
1c: SCOP_d2ihvd1 (D:198-374)
1d: SCOP_d2ihvb1 (B:198-374)
2a: SCOP_d2ihva3 (A:375-573)
2b: SCOP_d2ihvc3 (C:375-561)
2c: SCOP_d2ihvd3 (D:375-573)
2d: SCOP_d2ihvb3 (B:375-573)
3a: SCOP_d2ihva2 (A:11-197)
3b: SCOP_d2ihvc1 (C:11-197)
3c: SCOP_d2ihvd2 (D:11-197)
3d: SCOP_d2ihvb2 (B:11-197)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
Pyruvate oxidase and decarboxylase, middle domain
(74)
Protein domain
:
Carboxyethylarginine synthase
(6)
Streptomyces clavuligerus [TaxId: 1901]
(6)
1a
d2ihva1
A:198-374
1b
d2ihvc2
C:198-374
1c
d2ihvd1
D:198-374
1d
d2ihvb1
B:198-374
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
Pyruvate oxidase and decarboxylase PP module
(43)
Protein domain
:
Carboxyethylarginine synthase
(6)
Streptomyces clavuligerus [TaxId: 1901]
(6)
2a
d2ihva3
A:375-573
2b
d2ihvc3
C:375-561
2c
d2ihvd3
D:375-573
2d
d2ihvb3
B:375-573
Family
:
Pyruvate oxidase and decarboxylase Pyr module
(43)
Protein domain
:
Carboxyethylarginine synthase
(6)
Streptomyces clavuligerus [TaxId: 1901]
(6)
3a
d2ihva2
A:11-197
3b
d2ihvc1
C:11-197
3c
d2ihvd2
D:11-197
3d
d2ihvb2
B:11-197
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2ihvA03 (A:360-573)
1b: CATH_2ihvD03 (D:360-573)
1c: CATH_2ihvC03 (C:360-561)
1d: CATH_2ihvA01 (A:11-195)
1e: CATH_2ihvB01 (B:11-195)
1f: CATH_2ihvC01 (C:11-195)
1g: CATH_2ihvD01 (D:11-195)
1h: CATH_2ihvB03 (B:360-573)
2a: CATH_2ihvA02 (A:196-359)
2b: CATH_2ihvB02 (B:196-359)
2c: CATH_2ihvC02 (C:196-359)
2d: CATH_2ihvD02 (D:196-359)
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)
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)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Streptomyces clavuligerus. Organism_taxid: 1901.
(3)
1a
2ihvA03
A:360-573
1b
2ihvD03
D:360-573
1c
2ihvC03
C:360-561
1d
2ihvA01
A:11-195
1e
2ihvB01
B:11-195
1f
2ihvC01
C:11-195
1g
2ihvD01
D:11-195
1h
2ihvB03
B:360-573
Homologous Superfamily
:
TPP-binding domain
(120)
Streptomyces clavuligerus. Organism_taxid: 1901.
(3)
2a
2ihvA02
A:196-359
2b
2ihvB02
B:196-359
2c
2ihvC02
C:196-359
2d
2ihvD02
D:196-359
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Atom Selection
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