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3PFD
Biol. Unit 3
Info
Asym.Unit (480 KB)
Biol.Unit 1 (469 KB)
Biol.Unit 2 (122 KB)
Biol.Unit 3 (121 KB)
Biol.Unit 4 (121 KB)
Biol.Unit 5 (123 KB)
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Title
:
CRYSTAL STRUCTURE OF AN ACYL-COA DEHYDROGENASE FROM MYCOBACTERIUM THERMORESISTIBILE BOUND TO REDUCED FLAVIN ADENINE DINUCLEOTIDE SOLVED BY COMBINED IODIDE ION SAD MR
Authors
:
Seattle Structural Genomics Center For Infectious Disease (S
Date
:
28 Oct 10 (Deposition) - 10 Nov 10 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A (1x)
Biol. Unit 3: B (1x)
Biol. Unit 4: C (1x)
Biol. Unit 5: D (1x)
Keywords
:
Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Dehydrogenase, De Novo Phase Determination, Iodide Ion Sad, Acyl Coa Dehydrogenase, Reduced Flavin Adenine Dinucleotide, Fad, Fatty Acid Metabolism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Abendroth, A. S. Gardberg, J. I. Robinson, J. S. Christensen, B. L. Staker, P. J. Myler, L. J. Stewart, T. E. Edwards
Sad Phasing Using Iodide Ions In A High-Throughput Structural Genomics Environment.
J. Struct. Funct. Genom. V. 12 83 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 29)
Info
All Hetero Components
1a: DIHYDROFLAVINE-ADENINE DINUCLEOTID... (FDAa)
1b: DIHYDROFLAVINE-ADENINE DINUCLEOTID... (FDAb)
1c: DIHYDROFLAVINE-ADENINE DINUCLEOTID... (FDAc)
1d: DIHYDROFLAVINE-ADENINE DINUCLEOTID... (FDAd)
2a: IODIDE ION (IODa)
2aa: IODIDE ION (IODaa)
2ab: IODIDE ION (IODab)
2ac: IODIDE ION (IODac)
2ad: IODIDE ION (IODad)
2ae: IODIDE ION (IODae)
2af: IODIDE ION (IODaf)
2ag: IODIDE ION (IODag)
2ah: IODIDE ION (IODah)
2ai: IODIDE ION (IODai)
2aj: IODIDE ION (IODaj)
2ak: IODIDE ION (IODak)
2al: IODIDE ION (IODal)
2am: IODIDE ION (IODam)
2an: IODIDE ION (IODan)
2ao: IODIDE ION (IODao)
2ap: IODIDE ION (IODap)
2aq: IODIDE ION (IODaq)
2ar: IODIDE ION (IODar)
2as: IODIDE ION (IODas)
2at: IODIDE ION (IODat)
2au: IODIDE ION (IODau)
2av: IODIDE ION (IODav)
2aw: IODIDE ION (IODaw)
2ax: IODIDE ION (IODax)
2ay: IODIDE ION (IODay)
2az: IODIDE ION (IODaz)
2b: IODIDE ION (IODb)
2ba: IODIDE ION (IODba)
2bb: IODIDE ION (IODbb)
2bc: IODIDE ION (IODbc)
2bd: IODIDE ION (IODbd)
2be: IODIDE ION (IODbe)
2bf: IODIDE ION (IODbf)
2bg: IODIDE ION (IODbg)
2bh: IODIDE ION (IODbh)
2bi: IODIDE ION (IODbi)
2bj: IODIDE ION (IODbj)
2bk: IODIDE ION (IODbk)
2bl: IODIDE ION (IODbl)
2bm: IODIDE ION (IODbm)
2bn: IODIDE ION (IODbn)
2bo: IODIDE ION (IODbo)
2bp: IODIDE ION (IODbp)
2bq: IODIDE ION (IODbq)
2br: IODIDE ION (IODbr)
2bs: IODIDE ION (IODbs)
2bt: IODIDE ION (IODbt)
2bu: IODIDE ION (IODbu)
2bv: IODIDE ION (IODbv)
2bw: IODIDE ION (IODbw)
2bx: IODIDE ION (IODbx)
2by: IODIDE ION (IODby)
2bz: IODIDE ION (IODbz)
2c: IODIDE ION (IODc)
2ca: IODIDE ION (IODca)
2cb: IODIDE ION (IODcb)
2cc: IODIDE ION (IODcc)
2cd: IODIDE ION (IODcd)
2ce: IODIDE ION (IODce)
2cf: IODIDE ION (IODcf)
2cg: IODIDE ION (IODcg)
2ch: IODIDE ION (IODch)
2ci: IODIDE ION (IODci)
2cj: IODIDE ION (IODcj)
2ck: IODIDE ION (IODck)
2cl: IODIDE ION (IODcl)
2cm: IODIDE ION (IODcm)
2cn: IODIDE ION (IODcn)
2co: IODIDE ION (IODco)
2cp: IODIDE ION (IODcp)
2cq: IODIDE ION (IODcq)
2cr: IODIDE ION (IODcr)
2cs: IODIDE ION (IODcs)
2ct: IODIDE ION (IODct)
2cu: IODIDE ION (IODcu)
2cv: IODIDE ION (IODcv)
2cw: IODIDE ION (IODcw)
2cx: IODIDE ION (IODcx)
2cy: IODIDE ION (IODcy)
2cz: IODIDE ION (IODcz)
2d: IODIDE ION (IODd)
2da: IODIDE ION (IODda)
2db: IODIDE ION (IODdb)
2dc: IODIDE ION (IODdc)
2dd: IODIDE ION (IODdd)
2de: IODIDE ION (IODde)
2e: IODIDE ION (IODe)
2f: IODIDE ION (IODf)
2g: IODIDE ION (IODg)
2h: IODIDE ION (IODh)
2i: IODIDE ION (IODi)
2j: IODIDE ION (IODj)
2k: IODIDE ION (IODk)
2l: IODIDE ION (IODl)
2m: IODIDE ION (IODm)
2n: IODIDE ION (IODn)
2o: IODIDE ION (IODo)
2p: IODIDE ION (IODp)
2q: IODIDE ION (IODq)
2r: IODIDE ION (IODr)
2s: IODIDE ION (IODs)
2t: IODIDE ION (IODt)
2u: IODIDE ION (IODu)
2v: IODIDE ION (IODv)
2w: IODIDE ION (IODw)
2x: IODIDE ION (IODx)
2y: IODIDE ION (IODy)
2z: IODIDE ION (IODz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FDA
1
Ligand/Ion
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
2
IOD
28
Ligand/Ion
IODIDE ION
[
close Hetero Component info
]
Sites
(23, 23)
Info
All Sites
01: AC1 (SOFTWARE)
02: CC5 (SOFTWARE)
03: CC6 (SOFTWARE)
04: CC7 (SOFTWARE)
05: CC8 (SOFTWARE)
06: CC9 (SOFTWARE)
07: DC1 (SOFTWARE)
08: DC2 (SOFTWARE)
09: DC3 (SOFTWARE)
10: DC4 (SOFTWARE)
11: DC5 (SOFTWARE)
12: DC6 (SOFTWARE)
13: DC7 (SOFTWARE)
14: DC8 (SOFTWARE)
15: DC9 (SOFTWARE)
16: EC1 (SOFTWARE)
17: EC2 (SOFTWARE)
18: EC3 (SOFTWARE)
19: EC4 (SOFTWARE)
20: EC5 (SOFTWARE)
21: EC6 (SOFTWARE)
22: EC7 (SOFTWARE)
23: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:132 , LEU A:134 , SER A:135 , GLY A:140 , SER A:141 , TRP A:165 , ILE A:166 , THR A:167 , LYS A:210 , ILE A:368 , TYR A:372 , THR A:375 , GLN A:377 , IOD A:421 , HOH A:437 , HOH A:451 , HOH A:469 , ARG B:277 , GLN B:279 , PHE B:280 , VAL B:284 , ASN B:287 , VAL B:290 , GLN B:346 , LEU B:347 , GLY B:349 , GLY B:350 , HOH B:468 , GLN D:288
BINDING SITE FOR RESIDUE FDA A 390
02
CC5
SOFTWARE
ARG A:277 , GLN A:279 , PHE A:280 , VAL A:284 , ASN A:287 , VAL A:290 , GLN A:346 , LEU A:347 , GLY A:349 , GLY A:350 , HOH A:497 , TYR B:132 , LEU B:134 , SER B:135 , GLY B:140 , SER B:141 , TRP B:165 , THR B:167 , LYS B:210 , ILE B:368 , TYR B:372 , THR B:375 , GLN B:377 , IOD B:398 , HOH B:431 , HOH B:456 , HOH B:467 , HOH B:475 , GLN C:288
BINDING SITE FOR RESIDUE FDA B 390
03
CC6
SOFTWARE
GLN B:377 , ARG B:380
BINDING SITE FOR RESIDUE IOD B 392
04
CC7
SOFTWARE
GLN B:377
BINDING SITE FOR RESIDUE IOD B 393
05
CC8
SOFTWARE
ASP B:296 , ARG C:380
BINDING SITE FOR RESIDUE IOD B 395
06
CC9
SOFTWARE
IOD B:397 , HOH C:491
BINDING SITE FOR RESIDUE IOD B 396
07
DC1
SOFTWARE
SER B:285 , ASP B:286 , IOD B:396
BINDING SITE FOR RESIDUE IOD B 397
08
DC2
SOFTWARE
GLU B:373 , FDA B:390
BINDING SITE FOR RESIDUE IOD B 398
09
DC3
SOFTWARE
ILE B:20 , ARG B:23
BINDING SITE FOR RESIDUE IOD B 400
10
DC4
SOFTWARE
HOH B:527
BINDING SITE FOR RESIDUE IOD B 401
11
DC5
SOFTWARE
IOD B:403
BINDING SITE FOR RESIDUE IOD B 402
12
DC6
SOFTWARE
ASP B:75 , IOD B:402
BINDING SITE FOR RESIDUE IOD B 403
13
DC7
SOFTWARE
GLU B:40 , PHE C:47
BINDING SITE FOR RESIDUE IOD B 407
14
DC8
SOFTWARE
LYS B:101 , HIS B:250
BINDING SITE FOR RESIDUE IOD B 410
15
DC9
SOFTWARE
LYS B:101 , HIS B:250 , IOD B:412
BINDING SITE FOR RESIDUE IOD B 411
16
EC1
SOFTWARE
LYS B:101 , IOD B:411
BINDING SITE FOR RESIDUE IOD B 412
17
EC2
SOFTWARE
ARG B:137 , SER B:162
BINDING SITE FOR RESIDUE IOD B 413
18
EC3
SOFTWARE
THR B:181
BINDING SITE FOR RESIDUE IOD B 414
19
EC4
SOFTWARE
ASP B:156
BINDING SITE FOR RESIDUE IOD B 415
20
EC5
SOFTWARE
ARG B:314 , GLU C:302
BINDING SITE FOR RESIDUE IOD B 417
21
EC6
SOFTWARE
ARG B:314
BINDING SITE FOR RESIDUE IOD B 418
22
EC7
SOFTWARE
GLN B:288 , TYR C:132 , LEU C:134 , SER C:135 , GLY C:140 , SER C:141 , TRP C:165 , ILE C:166 , THR C:167 , LYS C:210 , ILE C:368 , TYR C:372 , THR C:375 , GLN C:377 , IOD C:396 , HOH C:417 , HOH C:428 , HOH C:431 , ARG D:277 , GLN D:279 , PHE D:280 , ARG D:282 , VAL D:284 , ASN D:287 , VAL D:290 , GLN D:346 , LEU D:347 , GLY D:350 , HOH D:430
BINDING SITE FOR RESIDUE FDA C 390
23
EC8
SOFTWARE
ARG B:380 , ASP C:296
BINDING SITE FOR RESIDUE IOD C 391
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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Label:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3pfda2 (A:239-389)
1b: SCOP_d3pfdb2 (B:239-389)
1c: SCOP_d3pfdc2 (C:239-389)
1d: SCOP_d3pfdd2 (D:239-389)
2a: SCOP_d3pfda1 (A:18-238)
2b: SCOP_d3pfdb1 (B:18-238)
2c: SCOP_d3pfdc1 (C:19-238)
2d: SCOP_d3pfdd1 (D:18-238)
View:
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Classes
(
)
(
)
Folds
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
automated matches
(29)
Protein domain
:
automated matches
(29)
Mycobacterium thermoresistibile [TaxId: 1797]
(2)
1a
d3pfda2
A:239-389
1b
d3pfdb2
B:239-389
1c
d3pfdc2
C:239-389
1d
d3pfdd2
D:239-389
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Mycobacterium thermoresistibile [TaxId: 1797]
(2)
2a
d3pfda1
A:18-238
2b
d3pfdb1
B:18-238
2c
d3pfdc1
C:19-238
2d
d3pfdd1
D:18-238
[
close SCOP info
]
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
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Label:
Sorry, no Info available
[
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]
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Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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Asym.Unit (480 KB)
Header - Asym.Unit
Biol.Unit 1 (469 KB)
Header - Biol.Unit 1
Biol.Unit 2 (122 KB)
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Biol.Unit 3 (121 KB)
Header - Biol.Unit 3
Biol.Unit 4 (121 KB)
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