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3Q9F
Asym. Unit
Info
Asym.Unit (665 KB)
Biol.Unit 1 (119 KB)
Biol.Unit 2 (119 KB)
Biol.Unit 3 (118 KB)
Biol.Unit 4 (118 KB)
Biol.Unit 5 (119 KB)
Biol.Unit 6 (119 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF APAH COMPLEXED WITH CAPS
Authors
:
P. M. Lombardi, D. W. Christianson
Date
:
07 Jan 11 (Deposition) - 02 Mar 11 (Release) - 30 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,I (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,K (1x)
Biol. Unit 4: D,J (1x)
Biol. Unit 5: E,H (1x)
Biol. Unit 6: G,L (1x)
Keywords
:
Hdac, Polyamine, Arginase Fold, Deacetylase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. M. Lombardi, H. D. Angell, D. A. Whittington, E. F. Flynn, K. R. Rajashankar, D. W. Christianson
Structure Of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships With Eukaryotic Histone Deacetylases .
Biochemistry V. 50 1808 2011
[
close entry info
]
Hetero Components
(5, 68)
Info
All Hetero Components
1a: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSa)
1b: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSb)
1c: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSc)
1d: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSd)
1e: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSe)
1f: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSf)
1g: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSg)
1h: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSh)
1i: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSi)
1j: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSj)
1k: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSk)
1l: 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID (CXSl)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
2e: POTASSIUM ION (Ke)
2f: POTASSIUM ION (Kf)
2g: POTASSIUM ION (Kg)
2h: POTASSIUM ION (Kh)
2i: POTASSIUM ION (Ki)
2j: POTASSIUM ION (Kj)
2k: POTASSIUM ION (Kk)
2l: POTASSIUM ION (Kl)
2m: POTASSIUM ION (Km)
2n: POTASSIUM ION (Kn)
2o: POTASSIUM ION (Ko)
2p: POTASSIUM ION (Kp)
2q: POTASSIUM ION (Kq)
2r: POTASSIUM ION (Kr)
2s: POTASSIUM ION (Ks)
2t: POTASSIUM ION (Kt)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
3i: SODIUM ION (NAi)
3j: SODIUM ION (NAj)
3k: SODIUM ION (NAk)
3l: SODIUM ION (NAl)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
4e: PHOSPHATE ION (PO4e)
4f: PHOSPHATE ION (PO4f)
4g: PHOSPHATE ION (PO4g)
4h: PHOSPHATE ION (PO4h)
4i: PHOSPHATE ION (PO4i)
4j: PHOSPHATE ION (PO4j)
4k: PHOSPHATE ION (PO4k)
4l: PHOSPHATE ION (PO4l)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
5i: ZINC ION (ZNi)
5j: ZINC ION (ZNj)
5k: ZINC ION (ZNk)
5l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CXS
12
Ligand/Ion
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
2
K
20
Ligand/Ion
POTASSIUM ION
3
NA
12
Ligand/Ion
SODIUM ION
4
PO4
12
Ligand/Ion
PHOSPHATE ION
5
ZN
12
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(68, 68)
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)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
63: GC9 (SOFTWARE)
64: HC1 (SOFTWARE)
65: HC2 (SOFTWARE)
66: HC3 (SOFTWARE)
67: HC4 (SOFTWARE)
68: HC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:117 , HIS A:158 , HIS A:159 , GLY A:167 , TYR A:168 , ASP A:195 , HIS A:197 , PHE A:225 , ASP A:284 , GLY A:321 , ZN A:345 , HOH A:1304 , HOH A:1305
BINDING SITE FOR RESIDUE CXS A 401
02
AC2
SOFTWARE
HIS A:54 , GLY A:55 , ARG A:180 , HOH A:370
BINDING SITE FOR RESIDUE PO4 A 353
03
AC3
SOFTWARE
ASP A:193 , ASP A:195 , HIS A:197 , SER A:216 , LEU A:217
BINDING SITE FOR RESIDUE K A 342
04
AC4
SOFTWARE
PHE A:206 , ARG A:209 , VAL A:212 , THR A:243 , HOH A:376
BINDING SITE FOR RESIDUE NA A 343
05
AC5
SOFTWARE
PHE A:286 , GLU A:287 , ASP A:289 , SER A:292 , PHE A:294 , HOH A:745
BINDING SITE FOR RESIDUE K A 344
06
AC6
SOFTWARE
ASP A:195 , HIS A:197 , ASP A:284 , CXS A:401
BINDING SITE FOR RESIDUE ZN A 345
07
AC7
SOFTWARE
HIS B:158 , HIS B:159 , GLY B:167 , TYR B:168 , ASP B:195 , HIS B:197 , PHE B:225 , ASP B:284 , ILE B:291 , GLY B:321 , TYR B:323 , ZN B:344
BINDING SITE FOR RESIDUE CXS B 402
08
AC8
SOFTWARE
HIS B:54 , GLY B:55 , ARG B:180 , HOH B:364
BINDING SITE FOR RESIDUE PO4 B 352
09
AC9
SOFTWARE
ASP B:193 , ASP B:195 , HIS B:197 , SER B:216 , LEU B:217
BINDING SITE FOR RESIDUE K B 342
10
BC1
SOFTWARE
PHE B:206 , ARG B:209 , VAL B:212 , THR B:243 , HOH B:347 , HOH B:794
BINDING SITE FOR RESIDUE NA B 343
11
BC2
SOFTWARE
ASP B:195 , HIS B:197 , ASP B:284 , CXS B:402
BINDING SITE FOR RESIDUE ZN B 344
12
BC3
SOFTWARE
HIS C:158 , HIS C:159 , GLY C:167 , TYR C:168 , ASP C:195 , HIS C:197 , PHE C:225 , ASP C:284 , GLY C:321 , ZN C:345 , HOH C:1301
BINDING SITE FOR RESIDUE CXS C 403
13
BC4
SOFTWARE
HIS C:54 , GLY C:55 , ARG C:180 , HOH C:475 , HOH C:476
BINDING SITE FOR RESIDUE PO4 C 353
14
BC5
SOFTWARE
ASP C:193 , ASP C:195 , HIS C:197 , SER C:216 , LEU C:217
BINDING SITE FOR RESIDUE K C 342
15
BC6
SOFTWARE
PHE C:206 , ARG C:209 , VAL C:212 , THR C:243 , HOH C:366
BINDING SITE FOR RESIDUE NA C 343
16
BC7
SOFTWARE
PHE C:286 , GLU C:287 , ASP C:289 , SER C:292 , PHE C:294 , HOH C:1274
BINDING SITE FOR RESIDUE K C 344
17
BC8
SOFTWARE
ASP C:195 , HIS C:197 , ASP C:284 , CXS C:403
BINDING SITE FOR RESIDUE ZN C 345
18
BC9
SOFTWARE
GLU D:117 , HIS D:158 , HIS D:159 , GLY D:167 , TYR D:168 , ASP D:195 , HIS D:197 , PHE D:225 , ASP D:284 , GLY D:321 , ZN D:345
BINDING SITE FOR RESIDUE CXS D 404
19
CC1
SOFTWARE
HIS D:54 , ARG D:180 , HOH D:364
BINDING SITE FOR RESIDUE PO4 D 352
20
CC2
SOFTWARE
ASP D:193 , ASP D:195 , HIS D:197 , SER D:216 , LEU D:217
BINDING SITE FOR RESIDUE K D 342
21
CC3
SOFTWARE
PHE D:206 , ARG D:209 , VAL D:212 , THR D:243 , HOH D:366
BINDING SITE FOR RESIDUE NA D 343
22
CC4
SOFTWARE
PHE D:286 , GLU D:287 , ASP D:289 , SER D:292 , PHE D:294 , HOH D:1275
BINDING SITE FOR RESIDUE K D 344
23
CC5
SOFTWARE
ASP D:195 , HIS D:197 , ASP D:284 , CXS D:404
BINDING SITE FOR RESIDUE ZN D 345
24
CC6
SOFTWARE
HIS E:158 , HIS E:159 , GLY E:167 , TYR E:168 , ASP E:195 , HIS E:197 , PHE E:225 , ASP E:284 , ILE E:291 , GLY E:321 , TYR E:323 , ZN E:345 , HOH E:1003
BINDING SITE FOR RESIDUE CXS E 405
25
CC7
SOFTWARE
HIS E:54 , GLY E:55 , ARG E:180 , HOH E:477
BINDING SITE FOR RESIDUE PO4 E 353
26
CC8
SOFTWARE
ASP E:193 , ASP E:195 , HIS E:197 , SER E:216 , LEU E:217
BINDING SITE FOR RESIDUE K E 342
27
CC9
SOFTWARE
PHE E:206 , ARG E:209 , VAL E:212 , THR E:243 , HOH E:359 , HOH E:558
BINDING SITE FOR RESIDUE NA E 343
28
DC1
SOFTWARE
PHE E:286 , GLU E:287 , ASP E:289 , SER E:292 , PHE E:294 , HOH E:1288 , HOH E:1289
BINDING SITE FOR RESIDUE K E 344
29
DC2
SOFTWARE
ASP E:195 , HIS E:197 , ASP E:284 , CXS E:405
BINDING SITE FOR RESIDUE ZN E 345
30
DC3
SOFTWARE
HIS F:158 , HIS F:159 , GLY F:167 , TYR F:168 , ASP F:195 , HIS F:197 , PHE F:225 , ASP F:284 , GLY F:321 , ZN F:345
BINDING SITE FOR RESIDUE CXS F 406
31
DC4
SOFTWARE
HIS F:54 , GLY F:55 , ARG F:180 , HOH F:364 , HOH F:366
BINDING SITE FOR RESIDUE PO4 F 352
32
DC5
SOFTWARE
ASP F:193 , ASP F:195 , HIS F:197 , SER F:216 , LEU F:217
BINDING SITE FOR RESIDUE K F 342
33
DC6
SOFTWARE
PHE F:206 , ARG F:209 , VAL F:212 , THR F:243 , HOH F:367
BINDING SITE FOR RESIDUE NA F 343
34
DC7
SOFTWARE
PHE F:286 , GLU F:287 , ASP F:289 , SER F:292 , PHE F:294
BINDING SITE FOR RESIDUE K F 344
35
DC8
SOFTWARE
ASP F:195 , HIS F:197 , ASP F:284 , CXS F:406
BINDING SITE FOR RESIDUE ZN F 345
36
DC9
SOFTWARE
HIS G:158 , HIS G:159 , GLY G:167 , TYR G:168 , ASP G:195 , HIS G:197 , PHE G:225 , ASP G:284 , GLY G:321 , TYR G:323 , ZN G:345 , HOH G:603 , HOH G:1004
BINDING SITE FOR RESIDUE CXS G 407
37
EC1
SOFTWARE
HIS G:54 , GLY G:55 , ARG G:180 , HOH G:360 , HOH G:472
BINDING SITE FOR RESIDUE PO4 G 353
38
EC2
SOFTWARE
ASP G:193 , ASP G:195 , HIS G:197 , SER G:216 , LEU G:217
BINDING SITE FOR RESIDUE K G 342
39
EC3
SOFTWARE
PHE G:206 , ARG G:209 , VAL G:212 , THR G:243 , HOH G:361
BINDING SITE FOR RESIDUE NA G 343
40
EC4
SOFTWARE
PHE G:286 , GLU G:287 , ASP G:289 , SER G:292 , PHE G:294 , HOH G:1286 , HOH G:1287
BINDING SITE FOR RESIDUE K G 344
41
EC5
SOFTWARE
ASP G:195 , HIS G:197 , ASP G:284 , CXS G:407
BINDING SITE FOR RESIDUE ZN G 345
42
EC6
SOFTWARE
GLU H:117 , HIS H:158 , HIS H:159 , GLY H:167 , TYR H:168 , ASP H:195 , HIS H:197 , ASP H:284 , GLY H:321 , ZN H:345
BINDING SITE FOR RESIDUE CXS H 408
43
EC7
SOFTWARE
HIS H:54 , GLY H:55 , ARG H:180
BINDING SITE FOR RESIDUE PO4 H 352
44
EC8
SOFTWARE
ASP H:193 , ASP H:195 , HIS H:197 , SER H:216 , LEU H:217
BINDING SITE FOR RESIDUE K H 342
45
EC9
SOFTWARE
PHE H:206 , ARG H:209 , VAL H:212 , THR H:243 , HOH H:362
BINDING SITE FOR RESIDUE NA H 343
46
FC1
SOFTWARE
PHE H:286 , GLU H:287 , ASP H:289 , SER H:292 , PHE H:294
BINDING SITE FOR RESIDUE K H 344
47
FC2
SOFTWARE
ASP H:195 , HIS H:197 , ASP H:284 , CXS H:408
BINDING SITE FOR RESIDUE ZN H 345
48
FC3
SOFTWARE
GLU I:117 , HIS I:158 , HIS I:159 , GLY I:167 , TYR I:168 , ASP I:195 , HIS I:197 , PHE I:225 , ASP I:284 , ILE I:291 , GLY I:321 , TYR I:323 , ZN I:344 , HOH I:536
BINDING SITE FOR RESIDUE CXS I 409
49
FC4
SOFTWARE
HIS I:54 , GLY I:55 , ARG I:180 , HOH I:479 , HOH I:480
BINDING SITE FOR RESIDUE PO4 I 353
50
FC5
SOFTWARE
ASP I:193 , ASP I:195 , HIS I:197 , SER I:216 , LEU I:217 , HIS I:218
BINDING SITE FOR RESIDUE K I 342
51
FC6
SOFTWARE
PHE I:206 , ARG I:209 , VAL I:212 , THR I:243 , HOH I:369
BINDING SITE FOR RESIDUE NA I 343
52
FC7
SOFTWARE
ASP I:195 , HIS I:197 , ASP I:284 , CXS I:409
BINDING SITE FOR RESIDUE ZN I 344
53
FC8
SOFTWARE
GLU J:117 , HIS J:158 , HIS J:159 , GLY J:167 , TYR J:168 , ASP J:195 , HIS J:197 , PHE J:225 , ASP J:284 , GLY J:321 , TYR J:323 , ZN J:344
BINDING SITE FOR RESIDUE CXS J 410
54
FC9
SOFTWARE
HIS J:54 , GLY J:55 , ARG J:180 , HOH J:377
BINDING SITE FOR RESIDUE PO4 J 352
55
GC1
SOFTWARE
ASP J:193 , ASP J:195 , HIS J:197 , SER J:216 , LEU J:217
BINDING SITE FOR RESIDUE K J 342
56
GC2
SOFTWARE
PHE J:206 , ARG J:209 , VAL J:212 , THR J:243 , HOH J:379
BINDING SITE FOR RESIDUE NA J 343
57
GC3
SOFTWARE
ASP J:195 , HIS J:197 , ASP J:284 , CXS J:410
BINDING SITE FOR RESIDUE ZN J 344
58
GC4
SOFTWARE
TYR K:19 , GLU K:117 , HIS K:158 , HIS K:159 , GLY K:167 , TYR K:168 , ASP K:195 , HIS K:197 , PHE K:225 , ASP K:284 , ILE K:291 , GLY K:321 , TYR K:323 , ZN K:344
BINDING SITE FOR RESIDUE CXS K 411
59
GC5
SOFTWARE
HIS K:54 , GLY K:55 , ARG K:180 , HOH K:365 , HOH K:473
BINDING SITE FOR RESIDUE PO4 K 353
60
GC6
SOFTWARE
ASP K:193 , ASP K:195 , HIS K:197 , SER K:216 , LEU K:217
BINDING SITE FOR RESIDUE K K 342
61
GC7
SOFTWARE
PHE K:206 , ARG K:209 , VAL K:212 , THR K:243 , HOH K:369
BINDING SITE FOR RESIDUE NA K 343
62
GC8
SOFTWARE
ASP K:195 , HIS K:197 , ASP K:284 , CXS K:411
BINDING SITE FOR RESIDUE ZN K 344
63
GC9
SOFTWARE
GLU L:117 , HIS L:158 , HIS L:159 , GLY L:167 , TYR L:168 , ASP L:195 , HIS L:197 , PHE L:225 , ASP L:284 , GLY L:321 , ZN L:345 , HOH L:1017 , HOH L:1299
BINDING SITE FOR RESIDUE CXS L 412
64
HC1
SOFTWARE
HIS L:54 , GLY L:55 , ARG L:180 , HOH L:372
BINDING SITE FOR RESIDUE PO4 L 352
65
HC2
SOFTWARE
ASP L:193 , ASP L:195 , HIS L:197 , SER L:216 , LEU L:217
BINDING SITE FOR RESIDUE K L 342
66
HC3
SOFTWARE
PHE L:206 , ARG L:209 , VAL L:212 , THR L:243 , THR L:244 , HOH L:373
BINDING SITE FOR RESIDUE NA L 343
67
HC4
SOFTWARE
PHE L:286 , GLU L:287 , ASP L:289 , SER L:292 , PHE L:294 , HOH L:1265
BINDING SITE FOR RESIDUE K L 344
68
HC5
SOFTWARE
ASP L:195 , HIS L:197 , ASP L:284 , CXS L:412
BINDING SITE FOR RESIDUE ZN L 345
[
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]
SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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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Asym.Unit (665 KB)
Header - Asym.Unit
Biol.Unit 1 (119 KB)
Header - Biol.Unit 1
Biol.Unit 2 (119 KB)
Header - Biol.Unit 2
Biol.Unit 3 (118 KB)
Header - Biol.Unit 3
Biol.Unit 4 (118 KB)
Header - Biol.Unit 4
Biol.Unit 5 (119 KB)
Header - Biol.Unit 5
Biol.Unit 6 (119 KB)
Header - Biol.Unit 6
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