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4K6O
Asym. Unit
Info
Asym.Unit (875 KB)
Biol.Unit 1 (864 KB)
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(1)
Title
:
X-RAY STRUCTURE URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH 6-METHYLURACIL AT 1.17 A RESOLUTION
Authors
:
I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date
:
16 Apr 13 (Deposition) - 07 May 14 (Release) - 14 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.17
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Rossmann Fold, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, M. V. Dontsova, T. A. Seregina, A. S. Mironov, C. Betzel, A. M. Mikhailov
Crystallization And Preliminary X-Ray Study Of Vibrio Cholerae Uridine Phosphorylase In Complex With 6-Methyluracil
Acta Crystallogr. , Sect. F V. 70 60 2014
[
close entry info
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Hetero Components
(8, 54)
Info
All Hetero Components
1a: 6-METHYLPYRIMIDINE-2,4-DIOL (6MUa)
1b: 6-METHYLPYRIMIDINE-2,4-DIOL (6MUb)
1c: 6-METHYLPYRIMIDINE-2,4-DIOL (6MUc)
1d: 6-METHYLPYRIMIDINE-2,4-DIOL (6MUd)
1e: 6-METHYLPYRIMIDINE-2,4-DIOL (6MUe)
1f: 6-METHYLPYRIMIDINE-2,4-DIOL (6MUf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
2i: CHLORIDE ION (CLi)
2j: CHLORIDE ION (CLj)
2k: CHLORIDE ION (CLk)
2l: CHLORIDE ION (CLl)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
4a: ETHANOL (EOHa)
4b: ETHANOL (EOHb)
4c: ETHANOL (EOHc)
4d: ETHANOL (EOHd)
4e: ETHANOL (EOHe)
4f: ETHANOL (EOHf)
4g: ETHANOL (EOHg)
5a: GLYCEROL (GOLa)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
6e: MAGNESIUM ION (MGe)
6f: MAGNESIUM ION (MGf)
6g: MAGNESIUM ION (MGg)
6h: MAGNESIUM ION (MGh)
6i: MAGNESIUM ION (MGi)
6j: MAGNESIUM ION (MGj)
6k: MAGNESIUM ION (MGk)
6l: MAGNESIUM ION (MGl)
6m: MAGNESIUM ION (MGm)
6n: MAGNESIUM ION (MGn)
6o: MAGNESIUM ION (MGo)
6p: MAGNESIUM ION (MGp)
7a: SODIUM ION (NAa)
7b: SODIUM ION (NAb)
7c: SODIUM ION (NAc)
7d: SODIUM ION (NAd)
8a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
8b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
8c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
8d: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6MU
6
Ligand/Ion
6-METHYLPYRIMIDINE-2,4-DIOL
2
CL
12
Ligand/Ion
CHLORIDE ION
3
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
4
EOH
7
Ligand/Ion
ETHANOL
5
GOL
1
Ligand/Ion
GLYCEROL
6
MG
16
Ligand/Ion
MAGNESIUM ION
7
NA
4
Ligand/Ion
SODIUM ION
8
TRS
4
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(54, 54)
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)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:44 , SER A:45 , HOH A:572 , HOH A:665
BINDING SITE FOR RESIDUE CL A 301
02
AC2
SOFTWARE
GLY A:25 , ASP A:26 , HOH A:478 , HOH A:491 , HOH B:531
BINDING SITE FOR RESIDUE CL A 302
03
AC3
SOFTWARE
THR A:93 , GLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , GLU A:195 , MET A:196 , ILE A:219 , HOH A:463 , HOH A:512 , HOH A:530 , HOH A:562
BINDING SITE FOR RESIDUE 6MU A 303
04
AC4
SOFTWARE
GLN A:180 , HOH A:496 , HOH A:499 , HOH A:535 , HOH A:543 , HOH A:600
BINDING SITE FOR RESIDUE MG A 304
05
AC5
SOFTWARE
HOH A:457 , HOH A:461 , HOH A:474 , HOH A:493 , HOH A:519 , HOH A:546
BINDING SITE FOR RESIDUE MG A 305
06
AC6
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 306
07
AC7
SOFTWARE
MET A:125 , GLU A:126 , HOH A:487 , MET F:125
BINDING SITE FOR RESIDUE EDO A 307
08
AC8
SOFTWARE
ARG A:178 , HOH A:584 , HOH A:611 , LEU B:120 , HOH B:431 , HOH B:435
BINDING SITE FOR RESIDUE EOH A 308
09
AC9
SOFTWARE
PHE A:133 , HOH A:519 , HOH A:602 , THR F:110 , HOH F:440
BINDING SITE FOR RESIDUE CL A 309
10
BC1
SOFTWARE
GLY B:25 , ASP B:26 , HOH B:543 , HOH B:646 , HOH B:733
BINDING SITE FOR RESIDUE CL B 301
11
BC2
SOFTWARE
ASN B:221 , HOH B:593
BINDING SITE FOR RESIDUE CL B 302
12
BC3
SOFTWARE
THR B:93 , GLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , GLU B:195 , MET B:196 , ILE B:219 , ILE B:220 , TRS B:308 , HOH B:417
BINDING SITE FOR RESIDUE 6MU B 303
13
BC4
SOFTWARE
GLN B:180 , HOH B:471 , HOH B:500 , HOH B:510 , HOH B:563 , HOH B:598
BINDING SITE FOR RESIDUE MG B 304
14
BC5
SOFTWARE
HOH B:444 , HOH B:446 , HOH B:506 , HOH B:518 , HOH B:727
BINDING SITE FOR RESIDUE MG B 305
15
BC6
SOFTWARE
HOH B:456 , HOH B:463
BINDING SITE FOR RESIDUE MG B 306
16
BC7
SOFTWARE
ARG B:167 , THR B:170 , ARG B:174 , HOH B:404
BINDING SITE FOR RESIDUE NA B 307
17
BC8
SOFTWARE
HIS A:7 , ARG A:47 , ILE B:68 , THR B:93 , GLU B:195 , MET B:196 , GLU B:197 , 6MU B:303 , HOH B:402 , HOH B:521 , HOH B:576 , HOH B:698
BINDING SITE FOR RESIDUE TRS B 308
18
BC9
SOFTWARE
PRO B:99 , VAL B:101 , ASN B:102 , VAL B:103 , ASN B:221 , HOH B:593 , HOH B:622 , HOH B:629
BINDING SITE FOR RESIDUE EDO B 309
19
CC1
SOFTWARE
LEU A:120 , HOH A:431 , ARG B:178 , HOH B:428 , HOH B:618 , HOH C:647
BINDING SITE FOR RESIDUE EOH B 310
20
CC2
SOFTWARE
GLY C:25 , ASP C:26 , HOH C:786
BINDING SITE FOR RESIDUE CL C 301
21
CC3
SOFTWARE
ASN C:221 , HOH C:594
BINDING SITE FOR RESIDUE CL C 302
22
CC4
SOFTWARE
THR B:110 , HOH B:493 , PHE C:133 , HOH C:446 , HOH C:682
BINDING SITE FOR RESIDUE CL C 303
23
CC5
SOFTWARE
THR C:93 , GLY C:95 , PHE C:161 , GLN C:165 , ARG C:167 , GLU C:195 , MET C:196 , ILE C:220 , TRS C:309 , HOH C:403
BINDING SITE FOR RESIDUE 6MU C 304
24
CC6
SOFTWARE
GLN C:180 , HOH C:525 , HOH C:579 , HOH C:591 , HOH C:601 , HOH E:543
BINDING SITE FOR RESIDUE MG C 305
25
CC7
SOFTWARE
HOH C:603 , HOH C:624 , HOH C:692 , HOH C:754 , HOH C:758 , HOH C:789
BINDING SITE FOR RESIDUE MG C 306
26
CC8
SOFTWARE
HOH B:493 , HOH B:527 , HOH C:439 , HOH C:444 , HOH C:450 , HOH C:533
BINDING SITE FOR RESIDUE MG C 307
27
CC9
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 308
28
DC1
SOFTWARE
ILE C:68 , THR C:93 , GLU C:195 , MET C:196 , GLU C:197 , 6MU C:304 , HOH C:472 , HOH C:520 , HOH C:731 , HIS D:7 , ARG D:47
BINDING SITE FOR RESIDUE TRS C 309
29
DC2
SOFTWARE
VAL C:101 , ASN C:102 , VAL C:103 , ASN C:221 , HOH C:594 , HOH C:649 , HOH C:705
BINDING SITE FOR RESIDUE EOH C 310
30
DC3
SOFTWARE
HOH B:631 , ARG C:178 , HOH C:630 , HOH C:635 , LEU D:120 , HOH D:418 , HOH D:427
BINDING SITE FOR RESIDUE EOH C 311
31
DC4
SOFTWARE
ARG C:47 , HOH C:477 , HOH C:704 , GLY D:25 , ILE D:68 , ARG D:90 , MET D:196 , GLU D:197 , HOH D:670 , HOH D:821
BINDING SITE FOR RESIDUE GOL C 312
32
DC5
SOFTWARE
HOH C:523 , GLY D:25 , ASP D:26 , HOH D:559
BINDING SITE FOR RESIDUE CL D 301
33
DC6
SOFTWARE
THR D:93 , GLY D:95 , GLN D:165 , ARG D:167 , GLU D:195 , MET D:196 , HOH D:445 , HOH D:810
BINDING SITE FOR RESIDUE 6MU D 302
34
DC7
SOFTWARE
GLN D:180 , HOH D:464 , HOH D:498 , HOH D:499 , HOH D:544 , HOH D:631
BINDING SITE FOR RESIDUE MG D 303
35
DC8
SOFTWARE
HIS D:46 , HOH D:518 , HOH D:652 , HOH D:797 , HOH D:814
BINDING SITE FOR RESIDUE MG D 304
36
DC9
SOFTWARE
HOH D:439 , HOH D:442 , HOH D:480 , HOH D:755 , HOH D:757
BINDING SITE FOR RESIDUE MG D 305
37
EC1
SOFTWARE
MET D:125 , GLU D:126 , HOH D:534 , MET E:125 , GLU E:126
BINDING SITE FOR RESIDUE EDO D 306
38
EC2
SOFTWARE
LEU C:120 , HOH C:427 , HOH C:428 , ARG D:178 , HOH D:560 , HOH D:562 , HOH D:778
BINDING SITE FOR RESIDUE EOH D 307
39
EC3
SOFTWARE
GLY E:25 , ASP E:26 , ARG E:29 , HOH F:601
BINDING SITE FOR RESIDUE CL E 301
40
EC4
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 , ILE E:220 , TRS E:306 , HOH E:420
BINDING SITE FOR RESIDUE 6MU E 302
41
EC5
SOFTWARE
HOH A:795 , GLN E:180 , HOH E:654 , HOH E:681 , HOH E:728
BINDING SITE FOR RESIDUE MG E 303
42
EC6
SOFTWARE
GLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72
BINDING SITE FOR RESIDUE NA E 304
43
EC7
SOFTWARE
HIS E:7 , ARG E:47 , HOH E:486 , HOH E:526 , HOH E:799 , ILE F:68 , THR F:93 , GLU F:197 , 6MU F:303 , HOH F:831
BINDING SITE FOR RESIDUE TRS E 305
44
EC8
SOFTWARE
ILE E:68 , THR E:93 , GLU E:195 , MET E:196 , GLU E:197 , 6MU E:302 , HOH E:457 , HOH E:520 , HOH E:702 , HOH E:724 , HIS F:7 , ARG F:47
BINDING SITE FOR RESIDUE TRS E 306
45
EC9
SOFTWARE
HOH D:595 , ARG E:178 , HOH E:602 , LEU F:120 , HOH F:423 , HOH F:430
BINDING SITE FOR RESIDUE EOH E 307
46
FC1
SOFTWARE
HOH E:461 , HOH E:491 , HOH E:518 , HOH E:788 , HOH E:821
BINDING SITE FOR RESIDUE MG E 308
47
FC2
SOFTWARE
GLY F:25 , ASP F:26 , ARG F:29 , HOH F:805
BINDING SITE FOR RESIDUE CL F 301
48
FC3
SOFTWARE
ARG F:29 , ALA F:238 , ILE F:241 , HOH F:447 , HOH F:728
BINDING SITE FOR RESIDUE CL F 302
49
FC4
SOFTWARE
TRS E:305 , THR F:93 , GLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , PHE F:194 , GLU F:195 , MET F:196 , ILE F:220 , HOH F:416
BINDING SITE FOR RESIDUE 6MU F 303
50
FC5
SOFTWARE
GLN F:180 , HOH F:594 , HOH F:605 , HOH F:607 , HOH F:676 , HOH F:827
BINDING SITE FOR RESIDUE MG F 304
51
FC6
SOFTWARE
ASN F:102 , MG F:306 , HOH F:468 , HOH F:501
BINDING SITE FOR RESIDUE MG F 305
52
FC7
SOFTWARE
MG F:305 , HOH F:468 , HOH F:501 , HOH F:558
BINDING SITE FOR RESIDUE MG F 306
53
FC8
SOFTWARE
LYS E:3 , GLN E:82 , ASP F:169 , THR F:170 , PHE F:171 , HOH F:523
BINDING SITE FOR RESIDUE EDO F 307
54
FC9
SOFTWARE
LEU E:120 , HOH E:428 , HOH E:437 , ARG F:178 , HOH F:571 , HOH F:622
BINDING SITE FOR RESIDUE EOH F 308
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SAPs(SNPs)/Variants
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