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3PFD
Biol. Unit 5
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
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: BC9 (SOFTWARE)
03: EC7 (SOFTWARE)
04: GC5 (SOFTWARE)
05: GC6 (SOFTWARE)
06: GC7 (SOFTWARE)
07: GC8 (SOFTWARE)
08: GC9 (SOFTWARE)
09: HC1 (SOFTWARE)
10: HC2 (SOFTWARE)
11: HC3 (SOFTWARE)
12: HC4 (SOFTWARE)
13: HC5 (SOFTWARE)
14: HC6 (SOFTWARE)
15: HC7 (SOFTWARE)
16: HC8 (SOFTWARE)
17: HC9 (SOFTWARE)
18: IC1 (SOFTWARE)
19: IC2 (SOFTWARE)
20: IC3 (SOFTWARE)
21: IC4 (SOFTWARE)
22: IC5 (SOFTWARE)
23: IC6 (SOFTWARE)
24: IC7 (SOFTWARE)
25: IC8 (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
BC9
SOFTWARE
ASP A:296 , ARG D:380 , HOH D:431
BINDING SITE FOR RESIDUE IOD A 416
03
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
04
GC5
SOFTWARE
GLN A:288 , ARG C:277 , GLN C:279 , PHE C:280 , ARG C:282 , VAL C:284 , ASN C:287 , VAL C:290 , GLN C:346 , LEU C:347 , GLY C:350 , TYR D:132 , LEU D:134 , SER D:135 , GLY D:140 , SER D:141 , TRP D:165 , ILE D:166 , THR D:167 , LYS D:210 , ILE D:368 , TYR D:372 , THR D:375 , GLN D:377 , IOD D:410 , HOH D:424 , HOH D:438 , HOH D:464 , HOH D:492
BINDING SITE FOR RESIDUE FDA D 390
05
GC6
SOFTWARE
ARG D:385
BINDING SITE FOR RESIDUE IOD D 391
06
GC7
SOFTWARE
SER D:285 , ASP D:286
BINDING SITE FOR RESIDUE IOD D 393
07
GC8
SOFTWARE
PRO D:358 , HOH D:421 , HOH D:602
BINDING SITE FOR RESIDUE IOD D 395
08
GC9
SOFTWARE
GLN D:377
BINDING SITE FOR RESIDUE IOD D 396
09
HC1
SOFTWARE
GLN D:377 , HOH D:459
BINDING SITE FOR RESIDUE IOD D 397
10
HC2
SOFTWARE
ARG D:314 , HOH D:449
BINDING SITE FOR RESIDUE IOD D 398
11
HC3
SOFTWARE
ARG D:23
BINDING SITE FOR RESIDUE IOD D 399
12
HC4
SOFTWARE
ARG A:380 , ASP D:296
BINDING SITE FOR RESIDUE IOD D 401
13
HC5
SOFTWARE
ARG C:277 , LYS C:278 , GLU D:138
BINDING SITE FOR RESIDUE IOD D 402
14
HC6
SOFTWARE
IOD D:404
BINDING SITE FOR RESIDUE IOD D 403
15
HC7
SOFTWARE
ASP D:75 , IOD D:403
BINDING SITE FOR RESIDUE IOD D 404
16
HC8
SOFTWARE
LYS D:101 , IOD D:408
BINDING SITE FOR RESIDUE IOD D 407
17
HC9
SOFTWARE
LYS D:101 , HIS D:250 , IOD D:407
BINDING SITE FOR RESIDUE IOD D 408
18
IC1
SOFTWARE
HIS D:250
BINDING SITE FOR RESIDUE IOD D 409
19
IC2
SOFTWARE
GLU D:373 , FDA D:390
BINDING SITE FOR RESIDUE IOD D 410
20
IC3
SOFTWARE
TRP D:174 , HOH D:535
BINDING SITE FOR RESIDUE IOD D 411
21
IC4
SOFTWARE
ARG D:137 , SER D:162
BINDING SITE FOR RESIDUE IOD D 412
22
IC5
SOFTWARE
ASP D:231
BINDING SITE FOR RESIDUE IOD D 413
23
IC6
SOFTWARE
ASP D:156
BINDING SITE FOR RESIDUE IOD D 414
24
IC7
SOFTWARE
THR D:181
BINDING SITE FOR RESIDUE IOD D 416
25
IC8
SOFTWARE
GLY D:281 , HOH D:555
BINDING SITE FOR RESIDUE IOD D 417
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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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
[
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Exons
(0, 0)
Info
All Exons
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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
(
)
(
)
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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Sorry, no Info available
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Chain D
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)
Header - Biol.Unit 4
Biol.Unit 5 (123 KB)
Header - Biol.Unit 5
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