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1Q8F
Asym. Unit
Info
Asym.Unit (216 KB)
Biol.Unit 1 (208 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE E.COLI PYRIMIDINE NUCLEOSIDE HYDROLASE YEIK
Authors
:
B. Giabbai, M. Degano
Date
:
21 Aug 03 (Deposition) - 11 May 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Open Alpha-Beta Structure, Nh-Fold, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Giabbai, M. Degano
Crystal Structure To 1. 7 A Of The Escherichia Coli Pyrimidine Nucleoside Hydrolase Yeik, A Novel Candidate For Cancer Gene Therapy.
Structure V. 12 739 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 20)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
GOL
16
Ligand/Ion
GLYCEROL
[
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Sites
(20, 20)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:11 , ASP A:16 , VAL A:124 , ASP A:240 , GOL A:3001 , HOH A:3022 , HOH A:3026
BINDING SITE FOR RESIDUE CA A 2001
02
AC2
SOFTWARE
ASP B:11 , ASP B:16 , VAL B:124 , ASP B:240 , GOL B:3002 , HOH B:3028 , HOH B:3041
BINDING SITE FOR RESIDUE CA B 2002
03
AC3
SOFTWARE
ASP C:11 , ASP C:16 , VAL C:124 , ASP C:240 , GOL C:3003 , HOH C:3027 , HOH C:3047
BINDING SITE FOR RESIDUE CA C 2003
04
AC4
SOFTWARE
ASP D:11 , ASP D:16 , VAL D:124 , ASP D:240 , GOL D:3004 , HOH D:3023 , HOH D:3039
BINDING SITE FOR RESIDUE CA D 2004
05
AC5
SOFTWARE
ASP A:15 , VAL A:124 , MET A:150 , ASN A:158 , GLU A:164 , PHE A:165 , ASN A:166 , ASP A:240 , CA A:2001 , GOL A:3005 , HOH A:3022 , HOH A:3026
BINDING SITE FOR RESIDUE GOL A 3001
06
AC6
SOFTWARE
ASP B:15 , VAL B:124 , MET B:150 , ASN B:158 , GLU B:164 , PHE B:165 , ASN B:166 , HIS B:239 , ASP B:240 , CA B:2002 , GOL B:3006 , HOH B:3028 , HOH B:3041
BINDING SITE FOR RESIDUE GOL B 3002
07
AC7
SOFTWARE
ASP C:15 , VAL C:124 , MET C:150 , ASN C:158 , GLU C:164 , PHE C:165 , ASN C:166 , ASP C:240 , CA C:2003 , GOL C:3007 , HOH C:3027 , HOH C:3047 , HOH C:3071
BINDING SITE FOR RESIDUE GOL C 3003
08
AC8
SOFTWARE
ASP D:15 , VAL D:124 , MET D:150 , ASN D:158 , GLU D:164 , PHE D:165 , ASN D:166 , ASP D:240 , CA D:2004 , GOL D:3008 , HOH D:3023 , HOH D:3039
BINDING SITE FOR RESIDUE GOL D 3004
09
AC9
SOFTWARE
ASN A:40 , ALA A:78 , HIS A:82 , ASN A:158 , PHE A:159 , PHE A:165 , TYR A:231 , GOL A:3001 , HOH A:3095
BINDING SITE FOR RESIDUE GOL A 3005
10
BC1
SOFTWARE
ASN B:40 , ALA B:78 , HIS B:82 , ASN B:158 , PHE B:159 , PHE B:165 , TYR B:231 , GOL B:3002 , HOH B:3067 , HOH B:3088
BINDING SITE FOR RESIDUE GOL B 3006
11
BC2
SOFTWARE
ASN C:40 , ALA C:78 , ILE C:81 , HIS C:82 , ASN C:158 , PHE C:159 , PHE C:165 , TYR C:231 , GOL C:3003 , HOH C:3071 , HOH C:3158 , HOH C:3282
BINDING SITE FOR RESIDUE GOL C 3007
12
BC3
SOFTWARE
ASN D:40 , ALA D:78 , HIS D:82 , ASN D:158 , PHE D:159 , PHE D:165 , TYR D:231 , GOL D:3004 , HOH D:3108
BINDING SITE FOR RESIDUE GOL D 3008
13
BC4
SOFTWARE
GLN A:74 , GOL A:3015 , HOH A:3274
BINDING SITE FOR RESIDUE GOL A 3009
14
BC5
SOFTWARE
ARG A:135 , VAL A:176 , THR A:179 , HOH A:3091 , GOL B:3011
BINDING SITE FOR RESIDUE GOL A 3010
15
BC6
SOFTWARE
ARG A:135 , GOL A:3010 , GLN B:69 , PRO B:70 , ARG B:73 , GLN B:74 , GLN B:75
BINDING SITE FOR RESIDUE GOL B 3011
16
BC7
SOFTWARE
MET C:134 , ARG C:135 , VAL C:176 , THR C:179 , SER C:180 , GLN D:74 , GOL D:3014 , HOH D:3050
BINDING SITE FOR RESIDUE GOL C 3012
17
BC8
SOFTWARE
ARG C:135 , GOL C:3012 , GLN D:69 , PRO D:70 , ARG D:73 , GLN D:74 , GLN D:75 , HOH D:3311
BINDING SITE FOR RESIDUE GOL D 3014
18
BC9
SOFTWARE
GLN A:69 , PRO A:70 , ARG A:73 , GLN A:74 , GLN A:75 , GOL A:3009 , ARG B:135
BINDING SITE FOR RESIDUE GOL A 3015
19
CC1
SOFTWARE
GLN C:69 , PRO C:70 , ARG C:73 , GLN C:74 , GLN C:75 , HOH C:3298 , ARG D:135 , GOL D:3017 , HOH D:3239
BINDING SITE FOR RESIDUE GOL C 3016
20
CC2
SOFTWARE
GOL C:3016 , ARG D:135 , VAL D:176 , THR D:179 , HOH D:3040 , HOH D:3109
BINDING SITE FOR RESIDUE GOL D 3017
[
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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: IUNH (A:9-19,B:9-19,C:9-19,D:9-19)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IUNH
PS01247
Inosine-uridine preferring nucleoside hydrolase family signature.
RIHB_ECOLI
9-19
4
A:9-19
B:9-19
C:9-19
D:9-19
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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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1q8fa_ (A:)
1b: SCOP_d1q8fb_ (B:)
1c: SCOP_d1q8fc_ (C:)
1d: SCOP_d1q8fd_ (D:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleoside hydrolase
(27)
Superfamily
:
Nucleoside hydrolase
(27)
Family
:
Nucleoside hydrolase
(22)
Protein domain
:
Pyrimidine nucleoside hydrolase YeiK
(3)
Escherichia coli [TaxId: 562]
(3)
1a
d1q8fa_
A:
1b
d1q8fb_
B:
1c
d1q8fc_
C:
1d
d1q8fd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1q8fA00 (A:3-310)
1b: CATH_1q8fB00 (B:3-310)
1c: CATH_1q8fC00 (C:3-310)
1d: CATH_1q8fD00 (D:3-310)
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Classes
(
)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Inosine-uridine Nucleoside N-ribohydrolase; Chain A
(17)
Homologous Superfamily
:
Inosine-uridine Nucleoside N-ribohydrolase, chain A
(17)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1q8fA00
A:3-310
1b
1q8fB00
B:3-310
1c
1q8fC00
C:3-310
1d
1q8fD00
D:3-310
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_IU_nuc_hydro_1q8fD01 (D:3-309)
1b: PFAM_IU_nuc_hydro_1q8fD02 (D:3-309)
1c: PFAM_IU_nuc_hydro_1q8fD03 (D:3-309)
1d: PFAM_IU_nuc_hydro_1q8fD04 (D:3-309)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: IU_nuc_hydro]
(7)
Family
:
IU_nuc_hydro
(7)
Escherichia coli (strain K12)
(2)
1a
IU_nuc_hydro-1q8fD01
D:3-309
1b
IU_nuc_hydro-1q8fD02
D:3-309
1c
IU_nuc_hydro-1q8fD03
D:3-309
1d
IU_nuc_hydro-1q8fD04
D:3-309
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