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2Z3I
Asym. Unit
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Asym.Unit (98 KB)
Biol.Unit 1 (92 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BLASTICIDIN S DEAMINASE (BSD) MUTANT E56Q COMPLEXED WITH SUBSTRATE
Authors
:
T. Kumasaka, M. Yamamoto, M. Furuichi, M. Nakasako, M. Kimura, I. Yamag T. Ueki
Date
:
04 Jun 07 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hydrolase, Cytidine Deaminase Family, Tetramer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kumasaka, M. Yamamoto, M. Furuichi, M. Nakasako, A. H. Teh, M. Kimura, I. Yamaguchi, T. Ueki
Crystal Structures Of Blasticidin S Deaminase (Bsd): Implications For Dynamic Properties Of Catalytic Zinc
J. Biol. Chem. V. 282 37103 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: BLASTICIDIN S (BLSa)
1b: BLASTICIDIN S (BLSb)
1c: BLASTICIDIN S (BLSc)
1d: BLASTICIDIN S (BLSd)
2a: CACODYLATE ION (CACa)
2b: CACODYLATE ION (CACb)
2c: CACODYLATE ION (CACc)
2d: CACODYLATE ION (CACd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BLS
4
Ligand/Ion
BLASTICIDIN S
2
CAC
4
Ligand/Ion
CACODYLATE ION
3
ZN
4
Ligand/Ion
ZINC 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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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:25 , ASP A:26 , SER A:28 , VAL A:29 , ASN A:45 , TYR A:47 , CYS A:54 , ALA A:55 , GLN A:56 , ARG A:82 , SER A:86 , PRO A:87 , CYS A:88 , HOH A:3002 , HOH A:3091 , HOH A:3093 , HOH A:3138 , TYR B:126 , TRP B:128 , HOH B:3028 , TRP D:128 , GLY D:130
BINDING SITE FOR RESIDUE BLS A 2500
02
AC2
SOFTWARE
TYR A:126 , TRP A:128 , GLU B:25 , ASP B:26 , SER B:28 , VAL B:29 , ASN B:45 , TYR B:47 , CYS B:54 , ALA B:55 , GLN B:56 , ARG B:82 , SER B:86 , PRO B:87 , CYS B:88 , HOH B:3015 , HOH B:3088 , HOH B:3113 , HOH B:3137 , TRP C:128
BINDING SITE FOR RESIDUE BLS B 2501
03
AC3
SOFTWARE
GLY B:130 , GLU C:25 , ASP C:26 , SER C:28 , VAL C:29 , ASN C:45 , TYR C:47 , CYS C:54 , ALA C:55 , GLN C:56 , ARG C:82 , SER C:86 , PRO C:87 , CYS C:88 , HOH C:3028 , HOH C:3078 , HOH C:3098 , HOH C:3105 , HOH C:3133 , HOH C:3149 , TYR D:126 , TRP D:128
BINDING SITE FOR RESIDUE BLS C 2502
04
AC4
SOFTWARE
TRP A:128 , GLU A:129 , TYR C:126 , TRP C:128 , GLU C:129 , GLU D:25 , ASP D:26 , SER D:28 , VAL D:29 , ASN D:45 , TYR D:47 , CYS D:54 , ALA D:55 , GLN D:56 , ARG D:82 , SER D:86 , PRO D:87 , CYS D:88 , HOH D:3089 , HOH D:3093 , HOH D:3132 , HOH D:3139
BINDING SITE FOR RESIDUE BLS D 2503
05
AC5
SOFTWARE
CYS A:54 , CYS A:88 , CYS A:91 , HOH A:3063 , HOH A:3138
BINDING SITE FOR RESIDUE ZN A 2001
06
AC6
SOFTWARE
SER A:4 , GLU A:7 , CYS A:73 , ALA A:115
BINDING SITE FOR RESIDUE CAC A 3001
07
AC7
SOFTWARE
CYS B:54 , CYS B:88 , CYS B:91 , HOH B:3047 , HOH B:3141
BINDING SITE FOR RESIDUE ZN B 2002
08
AC8
SOFTWARE
SER B:4 , GLU B:7 , THR B:72 , CYS B:73 , LYS B:103 , ALA B:115 , HOH B:3021
BINDING SITE FOR RESIDUE CAC B 3002
09
AC9
SOFTWARE
CYS C:54 , CYS C:88 , CYS C:91 , HOH C:3063 , HOH C:3149
BINDING SITE FOR RESIDUE ZN C 2003
10
BC1
SOFTWARE
GLU C:7 , CYS C:73 , ILE C:105 , ALA C:115
BINDING SITE FOR RESIDUE CAC C 3003
11
BC2
SOFTWARE
CYS D:54 , CYS D:88 , CYS D:91 , HOH D:3049 , HOH D:3139
BINDING SITE FOR RESIDUE ZN D 2004
12
BC3
SOFTWARE
GLU D:6 , GLU D:7 , CYS D:73 , LYS D:103 , ALA D:115
BINDING SITE FOR RESIDUE CAC D 3004
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: CYT_DCMP_DEAMINASES_1 (A:54-95,B:54-95,C:54-95,D:54-95)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYT_DCMP_DEAMINASES_1
PS00903
Cytidine and deoxycytidylate deaminases zinc-binding region signature.
BSD_ASPTE
54-95
4
A:54-95
B:54-95
C:54-95
D:54-95
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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, 4)
Info
All SCOP Domains
1a: SCOP_d2z3ia_ (A:)
1b: SCOP_d2z3ib_ (B:)
1c: SCOP_d2z3ic_ (C:)
1d: SCOP_d2z3id_ (D:)
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Cytidine deaminase-like
(78)
Superfamily
:
Cytidine deaminase-like
(76)
Family
:
Cytidine deaminase
(22)
Protein domain
:
automated matches
(9)
Aspergillus terreus [TaxId: 33178]
(6)
1a
d2z3ia_
A:
1b
d2z3ib_
B:
1c
d2z3ic_
C:
1d
d2z3id_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_dCMP_cyt_deam_1_2z3iD01 (D:4-108)
1b: PFAM_dCMP_cyt_deam_1_2z3iD02 (D:4-108)
1c: PFAM_dCMP_cyt_deam_1_2z3iD03 (D:4-108)
1d: PFAM_dCMP_cyt_deam_1_2z3iD04 (D:4-108)
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Clan
:
CDA
(39)
Family
:
dCMP_cyt_deam_1
(28)
Aspergillus terreus
(5)
1a
dCMP_cyt_deam_1-2z3iD01
D:4-108
1b
dCMP_cyt_deam_1-2z3iD02
D:4-108
1c
dCMP_cyt_deam_1-2z3iD03
D:4-108
1d
dCMP_cyt_deam_1-2z3iD04
D:4-108
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Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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