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4H0Y
Asym. Unit
Info
Asym.Unit (267 KB)
Biol.Unit 1 (258 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NAD+-IA(E380S)-ACTIN COMPLEX
Authors
:
T. Tsurumura, M. Oda, M. Nagahama, H. Tsuge
Date
:
10 Sep 12 (Deposition) - 20 Feb 13 (Release) - 10 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Adp-Ribosyltransferase, Toxin-Structural Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Tsurumura, Y. Tsumori, H. Qiu, M. Oda, J. Sakurai, M. Nagahama, H. Tsuge
Arginine Adp-Ribosylation Mechanism Based On Structural Snapshots Of Iota-Toxin And Actin Complex
Proc. Natl. Acad. Sci. Usa V. 110 4267 2013
[
close entry info
]
Hetero Components
(6, 57)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: CALCIUM ION (CAa)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3ag: 1,2-ETHANEDIOL (EDOag)
3ah: 1,2-ETHANEDIOL (EDOah)
3ai: 1,2-ETHANEDIOL (EDOai)
3aj: 1,2-ETHANEDIOL (EDOaj)
3ak: 1,2-ETHANEDIOL (EDOak)
3al: 1,2-ETHANEDIOL (EDOal)
3am: 1,2-ETHANEDIOL (EDOam)
3an: 1,2-ETHANEDIOL (EDOan)
3ao: 1,2-ETHANEDIOL (EDOao)
3ap: 1,2-ETHANEDIOL (EDOap)
3aq: 1,2-ETHANEDIOL (EDOaq)
3ar: 1,2-ETHANEDIOL (EDOar)
3as: 1,2-ETHANEDIOL (EDOas)
3at: 1,2-ETHANEDIOL (EDOat)
3au: 1,2-ETHANEDIOL (EDOau)
3av: 1,2-ETHANEDIOL (EDOav)
3aw: 1,2-ETHANEDIOL (EDOaw)
3ax: 1,2-ETHANEDIOL (EDOax)
3ay: 1,2-ETHANEDIOL (EDOay)
3az: 1,2-ETHANEDIOL (EDOaz)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: LATRUNCULIN A (LARa)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
6a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
1
Ligand/Ion
CALCIUM ION
3
EDO
52
Ligand/Ion
1,2-ETHANEDIOL
4
LAR
1
Ligand/Ion
LATRUNCULIN A
5
NAD
1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(57, 57)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:251 , ARG A:295 , ARG A:296 , GLY A:298 , GLN A:300 , GLU A:301 , TYR A:333 , ASN A:335 , SER A:338 , THR A:339 , PHE A:349 , ARG A:352 , GLU A:378 , SER A:380 , EDO A:508 , EDO A:522 , HOH A:697 , HOH A:727 , HOH A:749 , EDO B:407
BINDING SITE FOR RESIDUE NAD A 501
02
AC2
SOFTWARE
ARG A:5 , TRP A:19 , GLU A:23 , ILE A:85 , ASP A:86 , HOH A:704
BINDING SITE FOR RESIDUE PO4 A 502
03
AC3
SOFTWARE
TYR A:294 , ARG A:296 , SER A:340 , GLY A:342 , SER A:343 , VAL A:344 , PHE A:349
BINDING SITE FOR RESIDUE EDO A 503
04
AC4
SOFTWARE
MET A:346 , SER A:347 , ALA A:348 , MET B:176 , ARG B:177
BINDING SITE FOR RESIDUE EDO A 504
05
AC5
SOFTWARE
TYR A:60 , ASP A:61 , MET A:346 , SER A:347 , HOH A:735 , LYS B:284
BINDING SITE FOR RESIDUE EDO A 505
06
AC6
SOFTWARE
ASP A:395 , SER A:396
BINDING SITE FOR RESIDUE EDO A 506
07
AC7
SOFTWARE
ALA A:101 , ASN A:103 , THR A:125 , GLU A:327 , EDO A:519 , HOH A:685
BINDING SITE FOR RESIDUE EDO A 507
08
AC8
SOFTWARE
ASP A:32 , THR A:33 , ILE A:331 , THR A:332 , NAD A:501 , HOH A:649
BINDING SITE FOR RESIDUE EDO A 508
09
AC9
SOFTWARE
THR A:164 , GLY A:165 , ILE A:179 , GLU A:180 , ASP A:182 , HOH A:610 , HOH A:648
BINDING SITE FOR RESIDUE EDO A 509
10
BC1
SOFTWARE
ILE A:17 , ASP A:174 , VAL A:175
BINDING SITE FOR RESIDUE EDO A 510
11
BC2
SOFTWARE
LYS A:11 , GLU A:143 , PRO A:144 , GLY A:145 , HOH A:677
BINDING SITE FOR RESIDUE EDO A 511
12
BC3
SOFTWARE
LYS A:362 , ASP A:363 , LYS B:238 , SER B:239
BINDING SITE FOR RESIDUE EDO A 512
13
BC4
SOFTWARE
TYR A:42 , SER A:46 , ASP A:138 , TYR A:169 , ASN A:171 , LYS A:176
BINDING SITE FOR RESIDUE EDO A 513
14
BC5
SOFTWARE
TYR A:60 , GLN A:63 , ASN A:345 , ALA A:350 , LYS A:351 , ASP A:399 , HOH A:630 , HOH A:638 , GLU B:276
BINDING SITE FOR RESIDUE EDO A 514
15
BC6
SOFTWARE
PHE A:59 , LYS A:398 , GLY A:400
BINDING SITE FOR RESIDUE EDO A 515
16
BC7
SOFTWARE
ARG A:107 , GLU A:109 , LYS A:150 , PRO A:151 , LYS A:198 , TYR A:200
BINDING SITE FOR RESIDUE EDO A 516
17
BC8
SOFTWARE
ASN A:90 , HIS A:157 , GLU A:204 , ALA A:205 , HOH A:682
BINDING SITE FOR RESIDUE EDO A 517
18
BC9
SOFTWARE
LYS A:159 , SER A:206 , ILE A:207
BINDING SITE FOR RESIDUE EDO A 518
19
CC1
SOFTWARE
ALA A:101 , ASN A:103 , LYS A:104 , EDO A:507
BINDING SITE FOR RESIDUE EDO A 519
20
CC2
SOFTWARE
GLN A:133 , ASP A:134 , TYR A:183 , ASP A:212 , ARG A:357
BINDING SITE FOR RESIDUE EDO A 520
21
CC3
SOFTWARE
LEU A:306 , SER A:308 , ASP A:312 , LYS A:353
BINDING SITE FOR RESIDUE EDO A 521
22
CC4
SOFTWARE
TYR A:246 , ASN A:255 , ARG A:295 , PHE A:336 , ILE A:337 , SER A:338 , NAD A:501 , HOH A:749
BINDING SITE FOR RESIDUE EDO A 522
23
CC5
SOFTWARE
ALA A:348 , ARG A:352 , MET B:269 , GLU B:270 , EDO B:407
BINDING SITE FOR RESIDUE EDO A 523
24
CC6
SOFTWARE
ASP A:61 , GLU A:65 , ASP A:215 , EDO A:525 , HOH A:647
BINDING SITE FOR RESIDUE EDO A 524
25
CC7
SOFTWARE
GLU A:70 , LYS A:74 , EDO A:524
BINDING SITE FOR RESIDUE EDO A 525
26
CC8
SOFTWARE
TYR A:62 , SER A:66 , TYR B:279
BINDING SITE FOR RESIDUE EDO A 526
27
CC9
SOFTWARE
GLN A:54 , ASP A:134 , PHE A:136 , LYS A:137 , GLN A:181 , HOH A:617 , HOH A:742
BINDING SITE FOR RESIDUE EDO A 527
28
DC1
SOFTWARE
SER A:210 , LEU A:211 , ASP A:212 , LYS A:219
BINDING SITE FOR RESIDUE EDO A 528
29
DC2
SOFTWARE
ATP B:402 , HOH B:522 , HOH B:523 , HOH B:525 , HOH B:526 , HOH B:527
BINDING SITE FOR RESIDUE CA B 401
30
DC3
SOFTWARE
GLY B:13 , SER B:14 , GLY B:15 , LEU B:16 , LYS B:18 , GLY B:156 , ASP B:157 , GLY B:158 , VAL B:159 , GLY B:182 , ARG B:210 , LYS B:213 , GLU B:214 , GLY B:301 , GLY B:302 , THR B:303 , MET B:305 , TYR B:306 , LYS B:336 , CA B:401 , EDO B:422 , HOH B:517 , HOH B:519 , HOH B:522 , HOH B:523 , HOH B:527 , HOH B:528 , HOH B:562 , HOH B:563
BINDING SITE FOR RESIDUE ATP B 402
31
DC4
SOFTWARE
GLY B:15 , LEU B:16 , PRO B:32 , ASP B:56 , GLN B:59 , ARG B:62 , LEU B:67 , TYR B:69 , ASP B:157 , ARG B:183 , THR B:186 , ARG B:206 , GLU B:207 , ARG B:210 , EDO B:420 , HOH B:559
BINDING SITE FOR RESIDUE LAR B 403
32
DC5
SOFTWARE
HIS B:73 , GLY B:158 , ASP B:179 , ASP B:184 , HOH B:585
BINDING SITE FOR RESIDUE EDO B 404
33
DC6
SOFTWARE
ARG B:183 , ARG B:206
BINDING SITE FOR RESIDUE EDO B 405
34
DC7
SOFTWARE
ILE B:267 , HOH B:573 , HOH B:584
BINDING SITE FOR RESIDUE EDO B 406
35
DC8
SOFTWARE
GLY A:298 , PRO A:299 , GLN A:300 , ARG A:352 , NAD A:501 , EDO A:523 , GLY B:268 , GLU B:270 , HOH B:593
BINDING SITE FOR RESIDUE EDO B 407
36
DC9
SOFTWARE
SER B:141 , LEU B:142 , SER B:145 , VAL B:298 , MET B:299 , PRO B:332 , SER B:338
BINDING SITE FOR RESIDUE EDO B 408
37
EC1
SOFTWARE
MET B:283 , ARG B:290 , TYR B:294 , PRO B:322 , EDO B:426 , EDO B:428
BINDING SITE FOR RESIDUE EDO B 409
38
EC2
SOFTWARE
THR B:318 , ALA B:321 , PRO B:322 , SER B:323 , MET B:325 , ILE B:327
BINDING SITE FOR RESIDUE EDO B 410
39
EC3
SOFTWARE
PHE A:2 , GLU A:4 , EDO B:412
BINDING SITE FOR RESIDUE EDO B 411
40
EC4
SOFTWARE
GLU A:4 , ARG A:5 , LYS A:87 , HOH A:703 , SER B:145 , EDO B:411
BINDING SITE FOR RESIDUE EDO B 412
41
EC5
SOFTWARE
THR B:148 , THR B:149 , ASN B:296
BINDING SITE FOR RESIDUE EDO B 413
42
EC6
SOFTWARE
ARG B:62 , TYR B:166 , THR B:203 , ALA B:204 , ASP B:288 , ASP B:292 , HOH B:540
BINDING SITE FOR RESIDUE EDO B 414
43
EC7
SOFTWARE
CYS B:285 , ASP B:286 , HOH B:502 , HOH B:603
BINDING SITE FOR RESIDUE EDO B 415
44
EC8
SOFTWARE
GLU B:83 , HIS B:87 , PHE B:127 , EDO B:417
BINDING SITE FOR RESIDUE EDO B 416
45
EC9
SOFTWARE
TYR B:91 , GLU B:99 , THR B:126 , PHE B:127 , SER B:350 , EDO B:416 , HOH B:554
BINDING SITE FOR RESIDUE EDO B 417
46
FC1
SOFTWARE
PRO B:243 , ASP B:244 , EDO B:419
BINDING SITE FOR RESIDUE EDO B 418
47
FC2
SOFTWARE
TYR B:198 , SER B:199 , PHE B:200 , GLU B:205 , EDO B:418
BINDING SITE FOR RESIDUE EDO B 419
48
FC3
SOFTWARE
ARG B:210 , ASP B:211 , LAR B:403 , HOH B:565
BINDING SITE FOR RESIDUE EDO B 420
49
FC4
SOFTWARE
ARG B:196 , ALA B:230 , SER B:233 , GLU B:237 , GLY B:251 , ASN B:252 , HOH B:538
BINDING SITE FOR RESIDUE EDO B 421
50
FC5
SOFTWARE
LYS B:213 , GLU B:214 , CYS B:217 , MET B:305 , TYR B:306 , PRO B:307 , ATP B:402 , HOH B:517 , HOH B:608
BINDING SITE FOR RESIDUE EDO B 422
51
FC6
SOFTWARE
PHE B:262 , HIS B:275 , ARG B:312 , GLU B:316 , EDO B:425
BINDING SITE FOR RESIDUE EDO B 423
52
FC7
SOFTWARE
GLN B:263 , PRO B:264 , SER B:265 , EDO B:425 , HOH B:599
BINDING SITE FOR RESIDUE EDO B 424
53
FC8
SOFTWARE
LYS A:351 , PHE B:262 , ALA B:272 , GLY B:273 , HIS B:275 , GLU B:276 , EDO B:423 , EDO B:424
BINDING SITE FOR RESIDUE EDO B 425
54
FC9
SOFTWARE
TYR B:279 , MET B:283 , LEU B:320 , ALA B:321 , PRO B:322 , EDO B:409
BINDING SITE FOR RESIDUE EDO B 426
55
GC1
SOFTWARE
GLU A:65 , SER A:66 , ARG B:290
BINDING SITE FOR RESIDUE EDO B 427
56
GC2
SOFTWARE
VAL B:201 , THR B:202 , ILE B:287 , LYS B:291 , EDO B:409 , HOH B:569
BINDING SITE FOR RESIDUE EDO B 428
57
GC3
SOFTWARE
ALA B:135 , ILE B:136 , VAL B:139 , LEU B:346 , HOH B:555
BINDING SITE FOR RESIDUE EDO B 429
[
close Site info
]
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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;
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Sorry, no Info available
[
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Exons
(0, 0)
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d4h0ya1 (A:1-209)
1b: SCOP_d4h0ya2 (A:210-413)
2a: SCOP_d4h0yb1 (B:5-146)
2b: SCOP_d4h0yb2 (B:147-374)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ADP-ribosylation
(157)
Superfamily
:
ADP-ribosylation
(157)
Family
:
ADP-ribosylating toxins
(85)
Protein domain
:
automated matches
(21)
Clostridium perfringens [TaxId: 1502]
(6)
1a
d4h0ya1
A:1-209
1b
d4h0ya2
A:210-413
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
Actin/HSP70
(199)
Protein domain
:
Actin
(69)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(55)
2a
d4h0yb1
B:5-146
2b
d4h0yb2
B:147-374
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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