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Asym. Unit
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Asym.Unit (572 KB)
Biol.Unit 1 (565 KB)
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(1)
Title
:
X-RAY STRUCTURE URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH THYMIDINE AT 1.29 A RESOLUTION
Authors
:
I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date
:
01 Aug 13 (Deposition) - 31 Dec 14 (Release) - 28 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.29
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Rossmann Fold, Transferase, Cytoplasmic
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, V. V. Balaev, T. A. Seregina, A. S. Mironov, C. Betzel, A. M. Mikhailov
X-Ray Structures Of Uridine Phosphorylase From Vibrio Cholerae In Complexes With Uridine, Thymidine, Uracil, Thymine, And Phosphate Anion: Substrate Specificity Of Bacterial Uridine Phosphorylases
Crystallography Reports 2016
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Hetero Components
(6, 33)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: ETHANOL (EOHa)
3b: ETHANOL (EOHb)
3c: ETHANOL (EOHc)
3d: ETHANOL (EOHd)
3e: ETHANOL (EOHe)
3f: ETHANOL (EOHf)
3g: ETHANOL (EOHg)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
6a: THYMIDINE (THMa)
6b: THYMIDINE (THMb)
6c: THYMIDINE (THMc)
6d: THYMIDINE (THMd)
6e: THYMIDINE (THMe)
6f: THYMIDINE (THMf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
8
Ligand/Ion
CHLORIDE ION
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
EOH
7
Ligand/Ion
ETHANOL
4
MG
7
Ligand/Ion
MAGNESIUM ION
5
NA
3
Ligand/Ion
SODIUM ION
6
THM
6
Ligand/Ion
THYMIDINE
[
close Hetero Component info
]
Sites
(33, 33)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:93 , GLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , PHE A:194 , GLU A:195 , MET A:196 , GLU A:197 , ILE A:219 , HOH A:476 , HOH A:681 , HIS B:7 , ARG B:47
BINDING SITE FOR RESIDUE THM A 301
02
AC2
SOFTWARE
ARG A:178 , HOH A:601 , HOH A:676 , LEU B:120 , HOH B:425 , HOH B:715 , HOH F:616
BINDING SITE FOR RESIDUE EOH A 302
03
AC3
SOFTWARE
MET A:125 , GLU A:126 , HOH A:505 , MET F:125
BINDING SITE FOR RESIDUE EOH A 303
04
AC4
SOFTWARE
GLY A:25 , ASP A:26 , ARG A:29 , HOH A:493
BINDING SITE FOR RESIDUE CL A 304
05
AC5
SOFTWARE
GLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72
BINDING SITE FOR RESIDUE NA A 305
06
AC6
SOFTWARE
ASN A:221
BINDING SITE FOR RESIDUE CL A 306
07
AC7
SOFTWARE
GLN A:180 , HOH A:513 , HOH A:562 , HOH A:621 , HOH A:688 , HOH C:656
BINDING SITE FOR RESIDUE MG A 307
08
AC8
SOFTWARE
HIS A:7 , ARG A:47 , HOH A:516 , THR B:93 , GLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , PHE B:194 , GLU B:195 , MET B:196 , ILE B:220 , HOH B:426 , HOH B:442
BINDING SITE FOR RESIDUE THM B 301
09
AC9
SOFTWARE
MET B:125 , GLU C:126
BINDING SITE FOR RESIDUE EOH B 302
10
BC1
SOFTWARE
LEU A:120 , HOH A:417 , HOH A:421 , ARG B:178 , HOH B:539 , HOH B:716
BINDING SITE FOR RESIDUE EOH B 303
11
BC2
SOFTWARE
GLY B:25 , ASP B:26 , ARG B:29 , HOH B:459
BINDING SITE FOR RESIDUE CL B 304
12
BC3
SOFTWARE
GLN B:180 , HOH B:454 , HOH B:503 , HOH B:524 , HOH B:559
BINDING SITE FOR RESIDUE MG B 305
13
BC4
SOFTWARE
THR C:93 , GLY C:95 , PHE C:161 , GLN C:165 , ARG C:167 , PHE C:194 , GLU C:195 , MET C:196 , GLU C:197 , ILE C:220 , HOH C:410 , HOH C:494 , HOH C:591 , HIS D:7 , ARG D:47
BINDING SITE FOR RESIDUE THM C 301
14
BC5
SOFTWARE
HOH B:677 , ARG C:178 , HOH C:429 , HOH C:433 , HOH C:757 , HOH C:758 , LEU D:120
BINDING SITE FOR RESIDUE EDO C 302
15
BC6
SOFTWARE
GLY C:25 , ASP C:26 , ARG C:29 , HOH C:480
BINDING SITE FOR RESIDUE CL C 303
16
BC7
SOFTWARE
GLU C:48 , ILE C:68 , SER C:72 , GLU D:48 , ILE D:68 , SER D:72
BINDING SITE FOR RESIDUE NA C 304
17
BC8
SOFTWARE
MG C:306 , HOH C:486 , HOH C:492 , HOH C:561 , HOH C:660
BINDING SITE FOR RESIDUE MG C 305
18
BC9
SOFTWARE
ASN C:102 , MG C:305 , HOH C:486 , HOH C:488 , HOH C:492
BINDING SITE FOR RESIDUE MG C 306
19
CC1
SOFTWARE
HIS C:7 , ARG C:47 , ILE D:68 , THR D:93 , GLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , PHE D:194 , GLU D:195 , MET D:196 , GLU D:197 , ILE D:220 , HOH D:407 , HOH D:445 , HOH D:456 , HOH D:569
BINDING SITE FOR RESIDUE THM D 301
20
CC2
SOFTWARE
LEU C:120 , HOH C:437 , HOH C:761 , ARG D:178 , HOH D:697
BINDING SITE FOR RESIDUE EOH D 302
21
CC3
SOFTWARE
HOH C:590 , GLY D:25 , ASP D:26 , ARG D:29 , HOH D:466
BINDING SITE FOR RESIDUE CL D 303
22
CC4
SOFTWARE
MG D:305 , HOH D:470 , HOH D:528 , HOH D:568
BINDING SITE FOR RESIDUE MG D 304
23
CC5
SOFTWARE
ASN D:102 , MG D:304 , HOH D:470 , HOH D:528 , HOH D:666
BINDING SITE FOR RESIDUE MG D 305
24
CC6
SOFTWARE
THR E:93 , GLY E:95 , PHE E:161 , GLN E:165 , ARG E:167 , PHE E:194 , GLU E:195 , MET E:196 , GLU E:197 , HOH E:432 , HOH E:448 , HIS F:7 , ARG F:47
BINDING SITE FOR RESIDUE THM E 301
25
CC7
SOFTWARE
MET E:183 , GLN E:187 , HOH E:430 , HOH E:599 , HOH E:635
BINDING SITE FOR RESIDUE EDO E 302
26
CC8
SOFTWARE
ARG E:178 , HOH E:676 , HOH E:684 , HOH E:706 , LEU F:120 , HOH F:416 , HOH F:422
BINDING SITE FOR RESIDUE EOH E 303
27
CC9
SOFTWARE
GLY E:25 , ASP E:26 , ARG E:29 , HOH E:493 , HOH F:488
BINDING SITE FOR RESIDUE CL E 304
28
DC1
SOFTWARE
GLN E:180 , HOH E:468 , HOH E:562 , HOH E:574 , HOH E:619 , HOH E:622
BINDING SITE FOR RESIDUE MG E 305
29
DC2
SOFTWARE
HIS E:7 , ARG E:47 , THR F:93 , GLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , PHE F:194 , GLU F:195 , MET F:196 , GLU F:197 , ILE F:219 , ILE F:220 , HOH F:480 , HOH F:611
BINDING SITE FOR RESIDUE THM F 301
30
DC3
SOFTWARE
HOH A:600 , LEU E:120 , HOH E:421 , HOH E:423 , ARG F:178 , HOH F:598 , HOH F:685
BINDING SITE FOR RESIDUE EOH F 302
31
DC4
SOFTWARE
GLY F:25 , ASP F:26 , ARG F:29 , HOH F:585 , HOH F:686
BINDING SITE FOR RESIDUE CL F 303
32
DC5
SOFTWARE
GLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72
BINDING SITE FOR RESIDUE NA F 304
33
DC6
SOFTWARE
ASN F:221 , LYS F:225 , HOH F:569
BINDING SITE FOR RESIDUE CL F 305
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
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Info
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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
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Sorry, no Info available
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CATH Domains
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Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Info
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Sorry, no Info available
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