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4AC7
Asym. Unit
Info
Asym.Unit (283 KB)
Biol.Unit 1 (817 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE IN COMPLEX WITH CITRATE
Authors
:
S. Benini, P. Kosikowska, M. Cianci, A. Gonzalez Vara, L. Berlicki, S.
Date
:
14 Dec 11 (Deposition) - 16 Jan 13 (Release) - 03 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (3x)
Keywords
:
Hydrolase, Bacillus Pasteurii
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Benini, P. Kosikowska, M. Cianci, L. Mazzei, A. G. Vara, L. Berlicki S. Ciurli
The Crystal Structure Of Sporosarcina Pasteurii Urease In A Complex With Citrate Provides New Hints For Inhibitor Design.
J. Biol. Inorg. Chem. V. 18 391 2013
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 20)
Info
All Hetero Components
1a: N-CARBOXYMETHIONINE (CXMa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
3a: CITRATE ANION (FLCa)
4a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
5a: NICKEL (II) ION (NIa)
5b: NICKEL (II) ION (NIb)
6a: HYDROXIDE ION (OHa)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CXM
1
Mod. Amino Acid
N-CARBOXYMETHIONINE
2
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
3
FLC
1
Ligand/Ion
CITRATE ANION
4
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
5
NI
2
Ligand/Ion
NICKEL (II) ION
6
OH
1
Ligand/Ion
HYDROXIDE ION
7
SO4
4
Ligand/Ion
SULFATE ION
[
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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
GLY A:50 , LYS A:51 , THR A:52 , PHE A:86 , ASP A:88 , HOH A:2092 , HOH A:2093 , VAL C:309 , ASN C:310 , LYS C:559
BINDING SITE FOR RESIDUE EDO A1101
02
AC2
SOFTWARE
LYS A:29 , ASP A:67 , ASP A:68 , HOH A:2033 , HOH A:2038
BINDING SITE FOR RESIDUE EDO A1102
03
AC3
SOFTWARE
ASN A:4 , ALA A:6 , LYS A:10 , HOH A:2005 , HOH A:2084 , PHE C:568 , PHE C:570 , HOH C:2294
BINDING SITE FOR RESIDUE EDO A1103
04
AC4
SOFTWARE
ASP B:101 , HOH B:2141 , PRO C:229 , HOH C:2214
BINDING SITE FOR RESIDUE EDO B1127
05
AC5
SOFTWARE
ARG B:116
BINDING SITE FOR RESIDUE SO4 B1128
06
AC6
SOFTWARE
KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:601 , OH C:1571 , FLC C:1572
BINDING SITE FOR RESIDUE NI C 600
07
AC7
SOFTWARE
HIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:600 , OH C:1571 , FLC C:1572
BINDING SITE FOR RESIDUE NI C 601
08
AC8
SOFTWARE
HIS C:137 , KCX C:220 , HIS C:275 , ASP C:363 , NI C:600 , NI C:601 , FLC C:1572
BINDING SITE FOR RESIDUE OH C1571
09
AC9
SOFTWARE
HIS C:139 , LYS C:169 , ALA C:170 , KCX C:220 , HIS C:222 , ASP C:224 , HIS C:249 , GLY C:280 , ARG C:339 , ASP C:363 , ALA C:366 , MET C:367 , NI C:600 , NI C:601 , OH C:1571 , HOH C:2170 , HOH C:2209 , HOH C:2274
BINDING SITE FOR RESIDUE FLC C1572
10
BC1
SOFTWARE
ASP C:34 , THR C:36 , TYR C:38 , HOH C:2035 , HOH C:2050 , HOH C:2433
BINDING SITE FOR RESIDUE EDO C1573
11
BC2
SOFTWARE
ASP C:286 , ALA C:289 , ILE C:537 , ILE C:539 , HOH C:2234
BINDING SITE FOR RESIDUE EDO C1574
12
BC3
SOFTWARE
GLN B:41 , HOH B:2068 , GLY C:46 , LEU C:325 , HOH C:2276 , HOH C:2434
BINDING SITE FOR RESIDUE EDO C1575
13
BC4
SOFTWARE
TYR C:93 , GLU C:423 , GLN C:501 , ARG C:513 , ILE C:514 , HOH C:2435
BINDING SITE FOR RESIDUE EDO C1576
14
BC5
SOFTWARE
TYR C:35 , TYR C:83 , ILE C:97 , GLU C:429 , HOH C:2032 , HOH C:2436
BINDING SITE FOR RESIDUE EDO C1577
15
BC6
SOFTWARE
ARG C:62 , PRO C:177 , GLU C:181
BINDING SITE FOR RESIDUE EDO C1578
16
BC7
SOFTWARE
SER C:204 , ILE C:205 , HOH C:2084 , HOH C:2189 , HOH C:2194
BINDING SITE FOR RESIDUE SO4 C1579
17
BC8
SOFTWARE
VAL C:558 , LYS C:559 , GLU C:560 , HOH C:2422
BINDING SITE FOR RESIDUE SO4 C1580
18
BC9
SOFTWARE
LYS C:511
BINDING SITE FOR RESIDUE SO4 C1581
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: UREASE_1 (C:130-143)
2: UREASE_3 (C:132-570)
3: UREASE_2 (C:320-336)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UREASE_1
PS01120
Urease nickel ligands signature.
URE1_SPOPA
129-142
1
C:130-143
2
UREASE_3
PS51368
Urease domain profile.
URE1_SPOPA
131-569
1
C:132-570
3
UREASE_2
PS00145
Urease active site.
URE1_SPOPA
319-335
1
C:320-336
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d4ac7b_ (B:)
2a: SCOP_d4ac7c1 (C:1-131,C:435-483)
3a: SCOP_d4ac7a_ (A:)
4a: SCOP_d4ac7c2 (C:132-434,C:484-570)
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)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
Urease, beta-subunit
(40)
Family
:
Urease, beta-subunit
(40)
Protein domain
:
automated matches
(1)
Sporosarcina pasteurii [TaxId: 1474]
(1)
1a
d4ac7b_
B:
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
alpha-Subunit of urease
(40)
Protein domain
:
alpha-Subunit of urease
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
2a
d4ac7c1
C:1-131,C:435-483
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Urease, gamma-subunit
(42)
Superfamily
:
Urease, gamma-subunit
(42)
Family
:
Urease, gamma-subunit
(40)
Protein domain
:
Urease, gamma-subunit
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
3a
d4ac7a_
A:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
alpha-subunit of urease, catalytic domain
(40)
Protein domain
:
alpha-subunit of urease, catalytic domain
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
4a
d4ac7c2
C:132-434,C:484-570
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Chain C
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