507
Allinone(NBDC,DBCLS,PDBj,DDBJ)
1
(1)
(2)
(Structural Genomics)
(3)SNP
DnsSNPHOMCOS
HOMCOS
HOMCOS
( SeqID 44%)
(1fueA) (1ag9A)
SeqID = 44 %
RMSD = 1.2
1fueA 2:GKIGIFFGTDSGNAEAIAEKISKAIG--NAEVVDVAKASKEQFNGFTKVILVAPTAGAGD:59***** * ** * ** * * * * * * ** *** * ** *
1ag9A 2:AITGIFFGSDTGNTENIAKMIQKQLGKDVADVHDIAKSSKEDLEAYDILLLGIPTWYYGE:61
1fueA 60:LQTDWEDFLGTLEASD-FANKTIGLVGLGDQDTYSETFAEGIFHIYEKAK--AGKVVGQT:116* ** ** *** * * * * *** * * * * **
1ag9A 62:AQCDWDDFFPTLE-EIDFNGKLVALFGCGDQEDYAEYFCDALGTIRDIIEPRGATIVGHW:120
(
RMSD
(1ag9A)
NADPH P450 C (1ja1A2)
CheY(3chy)
(1d4aA)
44%, 1.2
8%, 4.4
(1fueA)
N
C 14%, 3.2
C
N
12 3 4 5
CNN
C
N
C
N
C
BLAST
PSI-BLAST
100
30%
BLASTE-value < 0.0001
PSI-BLASTE-value < 0.0001
0102030407025 15 535
(Sequence Identity)
(1)(DALIZMATRASRdis)(2)PSI-BLASTSeqID>=15%(3)(4)(5)(6)
50608090
LNVANGKSVIGPALLEEVWGSRD
M
N
I
AD
G
SV
V
GA L
QE
A W
FT
QD
PT
R
L
N
V
AN
G
SV
I
GL L
EE
V W
FS
QD
PA
R K
LNVANGKSVIGPALLEEVWFS-RD* * * ** ** * * ** **
MNIADG-SVVGPTALQEAWFTQRD
: .
BLAST, , . MODELLER, FAMS, .
(MODELLER)
Sequence ALIMSTKGFVSStructure LLLM---GFIT
(1)
(2)
Sequence AYVINDStructure AFVVTD AFVVTD AYVIND
MODELLER :http://www.salilab.org/modeller/modeller.html
MODELLER (http://www.salilab.org/modeller/)
[]
[NMR]
SeqID = 50 %
SeqID = 30 %
Ab initio
[]
SeqID = 100 %
Baker, D., Sali, A. Science (2001), 294, 93-96
AbinitioDe novo
MODELLER,SWISSMODEL ROSETTA,EVfold,
MODELLER, HOMCOS ZDOCK,HADDOCK,
MODELLER, HOMCOS,fkcombu
DOCK,AutoDock, sievgene,Glide,
PDBj1) GooglePDBj 2) PDBjSequence Navigator
3) [Search by sequence]UniProtCALL5_HUMAN
4) PDBBLASTPDB1ahrAsequence identity 51%
CALL5_HUMAN(Calmodulin-like protein 5)
UCSFChimeraModeller
Calmodulin (1ahr) Calmodulin-like protein 5(1ahr)
UCSF Chimera() ModellerGUI
Ca2+
UCSF ChimeraModeller 2015/6/13H27 PDBjing PDBj(http://pdbj.org/info/previous-workshop)
UCSFChimera
5000 RasMol, UCSF Chimera, PyMOL
[Tools][Structure Editing][AddH] [Tools][Structure Editing][Add Charge]
Auto Dock Vina [Surface/Binding Analysis][AutoDock Vina]
[Surface/Binding Analysis][ViewDock]
Cyclin-dependent protein kinase (CDK2)
ADPSubstrate PeptidePKTPKKAKKL
Cyclin A2
(1)
(2) 3D Complex of CDK2ADPCyclin A2 + Peptide(PDBcode:3qhw)
:TemplatebasedModeling
V
W
E
IE
I
N
GT
L
V
L
K
Q
V
F
TF
AT
V
F
E
IK
I
Q
GT
L
I
L
K
E
V
F
TF
AG
T
A L
Q
AE
LL
KL
K
VG
WK
D
T
T
A L
Q
LQ
LL
KL
K
IG
FK
D
T
V
F
E
IK
I
Q
GT
L
V
W
E
IE
I
N
GT
L
TGWVEIEINL..
TGWVEIEINL..
QLVVKTFAFT..
IVAWGKTDLQAE..
:TemplatebasedDocking
T
A L
Q
LQ
LLK
L
K
IGF
K
DT
VF
E
IKIQ
GT
L
I
L
K
EV
F
TF
AG
VW
E
IEIQ
GT
L
I
L
K
TV
F
TF
A
GD
I
L
K
TV
F
TF
A
G
VW
E
IEIQ
GT
L
D
VF
E
IKIQ
GT
L
I
L
K
EV
F
TF
AG
VW
E
IEIQ
GT
L
I
L
K
TV
F
TF
A
GD
S
A L
Q
LQ
LLK
L
K
IAS
DT
T
A L
Q
LQ
LLK
L
K
IGF
K
DT
S
A L
Q
LQ
LLK
L
K
IAS
DT
S
A L
Q
LQ
LLK
L
K
IAS
DT
-
50 %() 10%
Ca2+
Ca2+
(%) (%)
(%)
(%)
10%:Ca2+
HOMCOS :
PDB
A
B
PDBBLASTKCOMBU
MYB
HRXCrebbp
MYB
MRE-1
MRE-1
http://homcos.pdbj.orgHOMCOS
PDBBLAST
BLASTKCOMBU PDB
BLAST BLAST
BLAST KCOMBU
>1vwg_A
>1jsu_B
2g9xA1w98A1fq1B:
1vwg_1 A1 B12g9x_1 A1 B1:
KCOMBU
BLAST
TGWVEIEINL
SHLC39GBC:
SHL
GBC
C39
1vwg_1 A1 B12g9x_1 A1 B1:
PDB
PDB
CDK31) GoogleHOMCOS 2)
3) IDCDK3_HUMAN[SEARCH]
(i) PDB_ID+ (ii) PDB(iii) ID UniProt ID/AC
INSDCRefSeqprotein_id,(iv)
CDK3_HUMAN (Cyclin-dependent kinase 3)
ID PDB
HOMCOS
MEEPQSDPSVEPPLSQETFS
UniProtID P53_HUMAN []_[]
UniProtAC P04637Q15086
ACID
INSDC(DDBJ,EMBLEBI,NCBI)protein_id
AAG28785.1ABA29753.1EAW90143.1
DNAFEATURESCDSIDDDBJDAD
RefSeqprotein_id
NP_000537.3NP_001119584.1XP_011525440.1
NCBIdbSNP
INSDCDNAprotein_id
(CDK3)
E-value
(CDK3)Sequence-replaced 3D model
(CDK3_HUMAN)(1fin_C_1
ModellerModeller
CDK3CDK2
ContactBar(CDK3)
(%)
(CDK3)
CDK3CDK2
Cyclin A2
(CDK3)
b
Sequence-replaced modelModeller
CDK3
Cyclin A2
ContactBar(CDK3)
(%)
4QE, 4SPPDB
(CDK3)
4QE
(CDK3)
b
CDK3CDK2
Sequence-replaced modelModeller
SiteTable
UniProt(Feature Table)
(H:E:)
(%)
(1) acc
(2) observed aaSIFT score
3(CDK3)
PDBID3
(CDK3)
Cyclin A2
Met(Asn)
CDK3(CDK2)
SPIC_HUMAN
SPIC_HUMAN (Transcription factor Spi-C)
(SPIC)
PDB(Biological Unit) assembly_id=1
(SPIC)
PDB(Biological Unit) assembly_id=1
assembly_id=1
DnsSNP
3DnsSNP:nsSNP(1)1) GoogleNBDC 2)
3) Human Variation DB
3DnsSNP:nsSNP(2)4) Browse by disease name 5) Adrenoleukodystrophy
Wikipedia:Adrenoleukodystrophy, ALD1ALD
12XALDXX2X150%2
3DnsSNP:nsSNP(3)
dbSNP RefSeqID
3DnsSNP:nsSNP(4)
NP_000245.2919D(Asp)G(Gly) D
3DnsSNP:3D(1)1) GoogleHOMCOS 2)
3) IDNP_000245.2[SEARCH]
ID
NP_000245.2 919D(Asp)G(Gly)
3DnsSNP:3D(2) NP_000245.2 919D(Asp)G(Gly)
METH_HUMAN Methionine synthase, 5-methyltetrahydrofolate--homocysteine methyltransferase, Vitamin-B12 dependent methionine synthase. GN Name=MTR;
-!- FUNCTION: Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity). {ECO:0000250}. -!- CATALYTIC ACTIVITY: 5-methyltetrahydrofolate + L-homocysteine = tetrahydrofolate + L-methionine. CC -!- COFACTOR: Name=methyl(III)cobalamin; Xref=ChEBI:CHEBI:28115; -!- COFACTOR: Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};Note=Binds 1 zinc ion per subunit. {ECO:0000250}; -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via de novo pathway; L-methionine from L-homocysteine (MetH route): step 1/1.
3DnsSNP:3D(3) NP_000245.2 919D(Asp)G(Gly)
3DnsSNP:3D(4) NP_000245.2 919D(Asp)G(Gly)
COB:CO-METHYLCOBALAMIN
Co
919D(1bmtA893N)
919DCOB
COB
919D
COB
P_000245.2919DG
Adrenoleukodystrophy,ALDnsSNP(NP_000245.2919DG)
D14%G
55.1
COBG
E
IK
I
Q
GT
L
F
T
I
K
E
V
FV
L
F
AG
>1vwg_A
>1vwg_B
>2g9x_A
1vwgA2g9xA8atcA1fq5A:
1vwg_1 A1 B12g9x_1 A1 B11jsu_1 A1 B18atc_2 A1 B12fi5_1 E2 I1:
BLAST
BLAST
1vwg_1 A1 B1
V
W
E
IE
I
N
GT
L
V
L
K
Q
V
F
TF
AT
E
IK
I
Q
GT
L
F
T
I
K
E
V
FV
L
F
AG
TGWVEIEINL...
QLVVKTFAFT...
1vwgB2g9xB2fi5I2eufA:
B
A
Template-based Model(Sequence-replaced model)
V
W
E
IE
I
N
GT
L
T
V
K
Q
V
F
L
F
A
TV
W
E
IE
I
N
GT
L
T
V
K
Q
V
F
L
F
A
T
Template-based docking
B
A
or
or
orPDB
(21) GoogleHOMCOS 2)
CDK5_HUMAN Cyclin-dependent proten kinase 5CCNB1_HUMAN G2/mitotic-specific cyclin B1
3) AUNIPROT_IDCDK5_HUMANBUNIPROT_IDCCNB1_HUMAN
(i) PDB_ID+ (ii) PDB(iii) ID UniProt ID / AC
INSDCRefSeqprotein_id,(iv)
CDK5_HUMAN CCNB1_HUMAN
sequence-replaced 3D model
sequence-replaced modeltemplate 3D structure
ABPDBBLAST
Modeller(Win8)[1]
HOMCOSCDK5_HUMANCCNB1_HUMAN
Modeller
(model_complex.py) (alignment_complex.ali),(1h27_A_1_B_1.pdb)C:Usersguest01Downloads
Modeller(Win8)[2]
(4)
(5)MModeller
(6)
(7) cd []
cd C:Usersguest01Downloads
(8)dir
Modeller(Win8)[3]
(9) mod9.14 []Modellermod9.14 model_complex.py
(10)dirquery_complex.B99990001.pdbChimera
1) GoogleHOMCOS 2)
4au8A Cyclin-dependent proten kinase 52b9rA G2/mitotic-specific cyclin B1
3) APDB_ID4au8, CHAIN_IDABPDB_ID2b9r, CHAIN_IDA
(i) PDB_ID+ (ii) PDB(iii) UniProt ID (iv)
(2
ABPDBBLAST
4au8A (CDK5) 2b9rA (CCNB1)
template-based 3D docking model
sequence-replaced modeltemplate 3D structuretemplate-based 3D docking model
T
A L
Q
LQ
LLK
L
K
IGF
K
DT
>1vwg_A
2g9xA1jsuA1fq5A8atcA:
PDB
2g9x A1 B1(SHL)1jsu A1 B1(C39)8atc A1 B1(PLP)2fi5 E2 I2(ATP):
KCOMBU
BLAST
SHLC39GBC:
PDB
T
A L
Q
LQ
LLK
L
K
IGF
K
DT
fkcombu
SHL
GBCC39
SHL
TVAWGKTDLQL
2g9x_A1 B1
T
A L
QA E
LLK
L
R
VG WK
DT
or
T
A L
QA E
LLK
L
R
VG WK
DT
T
A L
Q
AE
LLK
L
R
VGW
K
DT
Template-based Model(Sequence-replaced model)
Template-based docking
>1vwg_B
>2g9x_A
or
2)
3) PROTEINUNIPROT_IDCDK3_HUMANCOMPOUNDPDB three letter ligand codeIRE
Iressa/Gefitinib (IRE)
1) GoogleHOMCOS
PDBBLAST PDBKCOMBU
(IRE) (DTQ)
(DTQ)
(IRE)
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