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2DV7
Asym. Unit
Info
Asym.Unit (99 KB)
Biol.Unit 1 (95 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LYS187 TO ARG MUTANT OF DIPHTHINE SYNTHASE
Authors
:
H. Mizutani, Y. Matsuura, K. Saraboji, S. M. Malathy Sony, M. N. Ponnus T. S. Kumarevel, N. Kunishima, Riken Structural Genomics/Proteom Initiative (Rsgi)
Date
:
28 Jul 06 (Deposition) - 28 Jan 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
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Reference
:
H. Mizutani, Y. Matsuura, K. Saraboji, S. M. Malathy Sony, M. N. Ponnuswamy, T. S. Kumarevel, N. Kunishima
Crystal Structure Of Diphthine Synthase From Pyrococcus Horikoshii Ot3
To Be Published
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
2a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
2c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
3a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
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No.
Name
Count
Type
Full Name
1
GOL
3
Ligand/Ion
GLYCEROL
2
MES
3
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3
SAH
1
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
4
SO4
5
Ligand/Ion
SULFATE ION
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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:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:46 , TYR B:128 , HIS B:243
BINDING SITE FOR RESIDUE SO4 B 1301
02
AC2
SOFTWARE
ARG A:60 , ALA A:91 , HOH A:1589 , LYS B:49
BINDING SITE FOR RESIDUE SO4 A 1302
03
AC3
SOFTWARE
TYR A:11 , SER A:211 , LEU A:212 , ASN A:213
BINDING SITE FOR RESIDUE SO4 A 1303
04
AC4
SOFTWARE
PRO B:257 , ARG B:258 , GLU B:259
BINDING SITE FOR RESIDUE SO4 B 1304
05
AC5
SOFTWARE
ARG B:46 , LYS B:129 , LYS B:241 , HIS B:243 , HOH B:1592 , HOH B:1619
BINDING SITE FOR RESIDUE SO4 B 1305
06
AC6
SOFTWARE
LEU A:10 , THR A:36 , SER A:37 , GLY A:86 , ASP A:87 , VAL A:90 , SER A:115 , ILE A:116 , PHE A:165 , LEU A:166 , LEU A:206 , ARG A:208 , ALA A:209 , PRO A:233 , HIS A:234 , ILE A:235 , HOH A:1533 , HOH A:1544
BINDING SITE FOR RESIDUE SAH A 1300
07
AC7
SOFTWARE
MET A:39 , THR A:42 , THR A:43 , LEU A:44 , VAL A:57
BINDING SITE FOR RESIDUE MES A 1501
08
AC8
SOFTWARE
GLY B:86 , SER B:115 , ILE B:116 , HOH B:1506
BINDING SITE FOR RESIDUE MES B 1502
09
AC9
SOFTWARE
ASP B:200 , TYR B:220 , LYS B:222 , GLU B:259
BINDING SITE FOR RESIDUE MES B 1503
10
BC1
SOFTWARE
TRP A:143 , LEU B:38 , MET B:39 , THR B:42 , THR B:43 , LEU B:44
BINDING SITE FOR RESIDUE GOL B 1401
11
BC2
SOFTWARE
TYR A:128 , LEU A:160 , HIS A:243 , HOH A:1639 , ASN B:66 , LYS B:132
BINDING SITE FOR RESIDUE GOL A 1402
12
BC3
SOFTWARE
THR A:43 , ARG A:46
BINDING SITE FOR RESIDUE GOL A 1403
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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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Exons
(0, 0)
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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_d2dv7a_ (A:)
1b: SCOP_d2dv7b_ (B:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Tetrapyrrole methylase
(104)
Superfamily
:
Tetrapyrrole methylase
(104)
Family
:
Tetrapyrrole methylase
(96)
Protein domain
:
Diphthine synthase, DphB
(82)
Pyrococcus horikoshii [TaxId: 53953]
(80)
1a
d2dv7a_
A:
1b
d2dv7b_
B:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2dv7A02 (A:115-265)
1b: CATH_2dv7B02 (B:115-265)
2a: CATH_2dv7A01 (A:1-114)
2b: CATH_2dv7B01 (B:1-114)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
(97)
Homologous Superfamily
:
Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
(97)
Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3.
(22)
1a
2dv7A02
A:115-265
1b
2dv7B02
B:115-265
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Cobalt-precorrin-4 Transmethylase; domain 1
(96)
Homologous Superfamily
:
Cobalt-precorrin-4 Transmethylase; Domain 1
(96)
Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3.
(22)
2a
2dv7A01
A:1-114
2b
2dv7B01
B:1-114
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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