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1PJL
Biol. Unit 1
Info
Asym.Unit (741 KB)
Biol.Unit 1 (363 KB)
Biol.Unit 2 (365 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN M-NAD-ME IN TERNARY COMPLEX WITH NAD AND LU3+
Authors
:
Z. Yang, R. Batra, D. L. Floyd, H. -C. Hung, G. -G. Chang, L. Tong
Date
:
03 Jun 03 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Yang, R. Batra, D. L. Floyd, H. -C. Hung, G. -G. Chang, L. Tong
Potent And Competitive Inhibition Of Malic Enzymes By Lanthanide Ions
Biochem. Biophys. Res. Commun. V. 274 440 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 64)
Info
All Hetero Components
1a: LUTETIUM (III) ION (LUa)
1b: LUTETIUM (III) ION (LUb)
1c: LUTETIUM (III) ION (LUc)
1d: LUTETIUM (III) ION (LUd)
1e: LUTETIUM (III) ION (LUe)
1f: LUTETIUM (III) ION (LUf)
1g: LUTETIUM (III) ION (LUg)
1h: LUTETIUM (III) ION (LUh)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2as: SELENOMETHIONINE (MSEas)
2at: SELENOMETHIONINE (MSEat)
2au: SELENOMETHIONINE (MSEau)
2av: SELENOMETHIONINE (MSEav)
2aw: SELENOMETHIONINE (MSEaw)
2ax: SELENOMETHIONINE (MSEax)
2ay: SELENOMETHIONINE (MSEay)
2az: SELENOMETHIONINE (MSEaz)
2b: SELENOMETHIONINE (MSEb)
2ba: SELENOMETHIONINE (MSEba)
2bb: SELENOMETHIONINE (MSEbb)
2bc: SELENOMETHIONINE (MSEbc)
2bd: SELENOMETHIONINE (MSEbd)
2be: SELENOMETHIONINE (MSEbe)
2bf: SELENOMETHIONINE (MSEbf)
2bg: SELENOMETHIONINE (MSEbg)
2bh: SELENOMETHIONINE (MSEbh)
2bi: SELENOMETHIONINE (MSEbi)
2bj: SELENOMETHIONINE (MSEbj)
2bk: SELENOMETHIONINE (MSEbk)
2bl: SELENOMETHIONINE (MSEbl)
2bm: SELENOMETHIONINE (MSEbm)
2bn: SELENOMETHIONINE (MSEbn)
2bo: SELENOMETHIONINE (MSEbo)
2bp: SELENOMETHIONINE (MSEbp)
2bq: SELENOMETHIONINE (MSEbq)
2br: SELENOMETHIONINE (MSEbr)
2bs: SELENOMETHIONINE (MSEbs)
2bt: SELENOMETHIONINE (MSEbt)
2bu: SELENOMETHIONINE (MSEbu)
2bv: SELENOMETHIONINE (MSEbv)
2bw: SELENOMETHIONINE (MSEbw)
2bx: SELENOMETHIONINE (MSEbx)
2by: SELENOMETHIONINE (MSEby)
2bz: SELENOMETHIONINE (MSEbz)
2c: SELENOMETHIONINE (MSEc)
2ca: SELENOMETHIONINE (MSEca)
2cb: SELENOMETHIONINE (MSEcb)
2cc: SELENOMETHIONINE (MSEcc)
2cd: SELENOMETHIONINE (MSEcd)
2ce: SELENOMETHIONINE (MSEce)
2cf: SELENOMETHIONINE (MSEcf)
2cg: SELENOMETHIONINE (MSEcg)
2ch: SELENOMETHIONINE (MSEch)
2ci: SELENOMETHIONINE (MSEci)
2cj: SELENOMETHIONINE (MSEcj)
2ck: SELENOMETHIONINE (MSEck)
2cl: SELENOMETHIONINE (MSEcl)
2cm: SELENOMETHIONINE (MSEcm)
2cn: SELENOMETHIONINE (MSEcn)
2co: SELENOMETHIONINE (MSEco)
2cp: SELENOMETHIONINE (MSEcp)
2cq: SELENOMETHIONINE (MSEcq)
2cr: SELENOMETHIONINE (MSEcr)
2cs: SELENOMETHIONINE (MSEcs)
2ct: SELENOMETHIONINE (MSEct)
2cu: SELENOMETHIONINE (MSEcu)
2cv: SELENOMETHIONINE (MSEcv)
2cw: SELENOMETHIONINE (MSEcw)
2cx: SELENOMETHIONINE (MSEcx)
2cy: SELENOMETHIONINE (MSEcy)
2cz: SELENOMETHIONINE (MSEcz)
2d: SELENOMETHIONINE (MSEd)
2da: SELENOMETHIONINE (MSEda)
2db: SELENOMETHIONINE (MSEdb)
2dc: SELENOMETHIONINE (MSEdc)
2dd: SELENOMETHIONINE (MSEdd)
2de: SELENOMETHIONINE (MSEde)
2df: SELENOMETHIONINE (MSEdf)
2dg: SELENOMETHIONINE (MSEdg)
2dh: SELENOMETHIONINE (MSEdh)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
3e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
3f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
3g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
3h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
3i: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADi)
3j: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADj)
3k: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADk)
3l: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADl)
3m: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADm)
3n: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADn)
3o: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADo)
3p: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LU
-1
Ligand/Ion
LUTETIUM (III) ION
2
MSE
56
Mod. Amino Acid
SELENOMETHIONINE
3
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:255 , ASP A:256 , ASP A:279
BINDING SITE FOR RESIDUE LU A 604
02
AC2
SOFTWARE
GLU B:1255 , ASP B:1256 , ASP B:1279
BINDING SITE FOR RESIDUE LU B 1604
03
AC3
SOFTWARE
GLU C:2255 , ASP C:2256 , ASP C:2279
BINDING SITE FOR RESIDUE LU C 2604
04
AC4
SOFTWARE
GLU D:3255 , ASP D:3256 , ASP D:3279
BINDING SITE FOR RESIDUE LU D 3604
05
AC9
SOFTWARE
ARG A:165 , ASN A:259 , THR A:283 , LEU A:310 , ALA A:312 , GLY A:313 , GLU A:314 , ALA A:315 , ASP A:345 , LYS A:346 , VAL A:392 , ALA A:393 , GLY A:394 , ALA A:395 , LEU A:398 , LEU A:419 , SER A:420 , ASN A:421 , GLY A:446 , GLY A:465 , ASN A:467
BINDING SITE FOR RESIDUE NAD A 601
06
BC1
SOFTWARE
HIS A:154 , GLY A:192 , ILE A:193 , ARG A:194 , ARG A:197 , ILE A:479 , LEU A:480 , ARG A:542 , TYR A:552 , ARG A:556
BINDING SITE FOR RESIDUE NAD A 602
07
BC2
SOFTWARE
ASN B:1259 , THR B:1283 , LEU B:1310 , ALA B:1312 , GLY B:1313 , GLU B:1314 , ALA B:1315 , ASP B:1345 , LYS B:1346 , VAL B:1392 , ALA B:1393 , GLY B:1394 , ALA B:1395 , LEU B:1398 , LEU B:1419 , SER B:1420 , ASN B:1421 , GLY B:1465 , ASN B:1467 , HOH B:8059
BINDING SITE FOR RESIDUE NAD B 1601
08
BC3
SOFTWARE
HIS B:1154 , LYS B:1156 , GLY B:1192 , ILE B:1193 , ARG B:1194 , ARG B:1197 , ILE B:1479 , LEU B:1480 , ASN B:1482 , ARG B:1542 , TYR B:1552 , ARG B:1556
BINDING SITE FOR RESIDUE NAD B 1602
09
BC4
SOFTWARE
ARG C:2165 , ASN C:2259 , THR C:2283 , LEU C:2310 , ALA C:2312 , GLY C:2313 , GLU C:2314 , ALA C:2315 , ASP C:2345 , LYS C:2346 , VAL C:2392 , ALA C:2393 , GLY C:2394 , ALA C:2395 , LEU C:2398 , LEU C:2419 , SER C:2420 , ASN C:2421 , GLY C:2446 , GLY C:2465 , ASN C:2467
BINDING SITE FOR RESIDUE NAD C 2601
10
BC5
SOFTWARE
HIS C:2154 , GLY C:2192 , ILE C:2193 , ARG C:2194 , ARG C:2197 , ILE C:2479 , LEU C:2480 , ASN C:2482 , ARG C:2542 , TYR C:2552 , ARG C:2556
BINDING SITE FOR RESIDUE NAD C 2602
11
BC6
SOFTWARE
ARG D:3165 , ASN D:3259 , THR D:3283 , LEU D:3310 , GLY D:3311 , ALA D:3312 , GLY D:3313 , GLU D:3314 , ALA D:3315 , ASP D:3345 , LYS D:3346 , VAL D:3392 , ALA D:3393 , GLY D:3394 , ALA D:3395 , LEU D:3398 , LEU D:3419 , SER D:3420 , ASN D:3421 , GLY D:3446 , GLY D:3465 , ASN D:3467
BINDING SITE FOR RESIDUE NAD D 3601
12
BC7
SOFTWARE
HIS D:3154 , LYS D:3156 , GLY D:3192 , ILE D:3193 , ARG D:3194 , ILE D:3479 , LEU D:3480 , ARG D:3542 , TYR D:3552 , ARG D:3556
BINDING SITE FOR RESIDUE NAD D 3602
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_034104 (P7114L, chain A/B/C/D/E/F/G/A/B/C/D, )
2: VAR_050017 (G7450E, chain A/B/C/D/E/F/G/A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_034104
P
114
L
MAOM_HUMAN
Polymorphism
16952692
A
B
C
D
E
F
G
A/B/C/D
P
114
1114
2114
3114
4114
5114
6114
7114
L
2
UniProt
VAR_050017
G
450
E
MAOM_HUMAN
Polymorphism
649224
A
B
C
D
E
F
G
A/B/C/D
G
450
1450
2450
3450
4450
5450
6450
7450
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: MALIC_ENZYMES (A:276-292,B:1276-1292,C:2276-2292,...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MALIC_ENZYMES
PS00331
Malic enzymes signature.
MAOM_HUMAN
276-292
4
A:276-292
B:1276-1292
C:2276-2292
D:3276-3292
-
-
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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, 16)
Info
All SCOP Domains
1a: SCOP_d1pjla2 (A:23-279)
1b: SCOP_d1pjlb2 (B:1023-1279)
1c: SCOP_d1pjlc2 (C:2023-2279)
1d: SCOP_d1pjld2 (D:3023-3279)
1e: SCOP_d1pjle2 (E:4023-4279)
1f: SCOP_d1pjlf2 (F:5023-5279)
1g: SCOP_d1pjlg2 (G:6023-6279)
1h: SCOP_d1pjlh2 (H:7023-7279)
2a: SCOP_d1pjla1 (A:280-573)
2b: SCOP_d1pjlb1 (B:1280-1573)
2c: SCOP_d1pjlc1 (C:2280-2573)
2d: SCOP_d1pjld1 (D:3280-3573)
2e: SCOP_d1pjle1 (E:4280-4573)
2f: SCOP_d1pjlf1 (F:5280-5573)
2g: SCOP_d1pjlg1 (G:6280-6573)
2h: SCOP_d1pjlh1 (H:7280-7573)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Malic enzyme N-domain
(14)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
1a
d1pjla2
A:23-279
1b
d1pjlb2
B:1023-1279
1c
d1pjlc2
C:2023-2279
1d
d1pjld2
D:3023-3279
1e
d1pjle2
E:4023-4279
1f
d1pjlf2
F:5023-5279
1g
d1pjlg2
G:6023-6279
1h
d1pjlh2
H:7023-7279
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
2a
d1pjla1
A:280-573
2b
d1pjlb1
B:1280-1573
2c
d1pjlc1
C:2280-2573
2d
d1pjld1
D:3280-3573
2e
d1pjle1
E:4280-4573
2f
d1pjlf1
F:5280-5573
2g
d1pjlg1
G:6280-6573
2h
d1pjlh1
H:7280-7573
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1pjlA01 (A:23-277)
1b: CATH_1pjlB01 (B:1023-1277)
1c: CATH_1pjlC01 (C:2023-2277)
1d: CATH_1pjlD01 (D:3023-3277)
1e: CATH_1pjlE01 (E:4023-4277)
1f: CATH_1pjlF01 (F:5023-5277)
1g: CATH_1pjlG01 (G:6023-6277)
1h: CATH_1pjlH01 (H:7023-7277)
2a: CATH_1pjlA02 (A:278-573)
2b: CATH_1pjlB02 (B:1278-1573)
2c: CATH_1pjlC02 (C:2278-2573)
2d: CATH_1pjlD02 (D:3278-3573)
2e: CATH_1pjlE02 (E:4278-4573)
2f: CATH_1pjlF02 (F:5278-5573)
2g: CATH_1pjlG02 (G:6278-6573)
2h: CATH_1pjlH02 (H:7278-7573)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain. Chain A
(17)
Human (Homo sapiens)
(11)
1a
1pjlA01
A:23-277
1b
1pjlB01
B:1023-1277
1c
1pjlC01
C:2023-2277
1d
1pjlD01
D:3023-3277
1e
1pjlE01
E:4023-4277
1f
1pjlF01
F:5023-5277
1g
1pjlG01
G:6023-6277
1h
1pjlH01
H:7023-7277
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1pjlA02
A:278-573
2b
1pjlB02
B:1278-1573
2c
1pjlC02
C:2278-2573
2d
1pjlD02
D:3278-3573
2e
1pjlE02
E:4278-4573
2f
1pjlF02
F:5278-5573
2g
1pjlG02
G:6278-6573
2h
1pjlH02
H:7278-7573
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_Malic_M_1pjlH01 (H:7280-7535)
1b: PFAM_Malic_M_1pjlH02 (H:7280-7535)
1c: PFAM_Malic_M_1pjlH03 (H:7280-7535)
1d: PFAM_Malic_M_1pjlH04 (H:7280-7535)
1e: PFAM_Malic_M_1pjlH05 (H:7280-7535)
1f: PFAM_Malic_M_1pjlH06 (H:7280-7535)
1g: PFAM_Malic_M_1pjlH07 (H:7280-7535)
1h: PFAM_Malic_M_1pjlH08 (H:7280-7535)
2a: PFAM_malic_1pjlH09 (H:7089-7270)
2b: PFAM_malic_1pjlH10 (H:7089-7270)
2c: PFAM_malic_1pjlH11 (H:7089-7270)
2d: PFAM_malic_1pjlH12 (H:7089-7270)
2e: PFAM_malic_1pjlH13 (H:7089-7270)
2f: PFAM_malic_1pjlH14 (H:7089-7270)
2g: PFAM_malic_1pjlH15 (H:7089-7270)
2h: PFAM_malic_1pjlH16 (H:7089-7270)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Malic_M
(9)
Homo sapiens (Human)
(5)
1a
Malic_M-1pjlH01
H:7280-7535
1b
Malic_M-1pjlH02
H:7280-7535
1c
Malic_M-1pjlH03
H:7280-7535
1d
Malic_M-1pjlH04
H:7280-7535
1e
Malic_M-1pjlH05
H:7280-7535
1f
Malic_M-1pjlH06
H:7280-7535
1g
Malic_M-1pjlH07
H:7280-7535
1h
Malic_M-1pjlH08
H:7280-7535
Clan
:
no clan defined [family: malic]
(9)
Family
:
malic
(9)
Homo sapiens (Human)
(5)
2a
malic-1pjlH09
H:7089-7270
2b
malic-1pjlH10
H:7089-7270
2c
malic-1pjlH11
H:7089-7270
2d
malic-1pjlH12
H:7089-7270
2e
malic-1pjlH13
H:7089-7270
2f
malic-1pjlH14
H:7089-7270
2g
malic-1pjlH15
H:7089-7270
2h
malic-1pjlH16
H:7089-7270
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