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1EFL
Asym. Unit
Info
Asym.Unit (375 KB)
Biol.Unit 1 (362 KB)
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(1)
Title
:
HUMAN MALIC ENZYME IN A QUATERNARY COMPLEX WITH NAD, MG, AND TARTRONATE
Authors
:
Z. Yang, D. L. Floyd, G. Loeber, L. Tong
Date
:
09 Feb 00 (Deposition) - 08 Mar 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Closed Form, Malic Enzyme, Complex, Tartronate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Yang, D. L. Floyd, G. Loeber, L. Tong
Structure Of A Closed Form Of Human Malic Enzyme And Implications For Catalytic Mechanism.
Nat. Struct. Biol. V. 7 251 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 72)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
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)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
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)
4a: TARTRONATE (TTNa)
4b: TARTRONATE (TTNb)
4c: TARTRONATE (TTNc)
4d: TARTRONATE (TTNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
4
Ligand/Ion
MAGNESIUM ION
2
MSE
56
Mod. Amino Acid
SELENOMETHIONINE
3
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4
TTN
4
Ligand/Ion
TARTRONATE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:165 , GLU A:255 , ASP A:256 , ASP A:279 , TTN A:603
BINDING SITE FOR RESIDUE MG A 604
02
AC2
SOFTWARE
ARG B:165 , LYS B:183 , GLU B:255 , ASP B:256 , ASP B:279 , TTN B:1603
BINDING SITE FOR RESIDUE MG B 1604
03
AC3
SOFTWARE
ARG C:165 , LYS C:183 , GLU C:255 , ASP C:256 , ASP C:279 , TTN C:2603
BINDING SITE FOR RESIDUE MG C 2604
04
AC4
SOFTWARE
ARG D:165 , GLU D:255 , ASP D:256 , ASP D:279 , TTN D:3603
BINDING SITE FOR RESIDUE MG D 3604
05
AC5
SOFTWARE
ARG A:165 , LEU A:167 , GLY A:168 , ASN A:259 , ASP A:279 , THR A:283 , LEU A:310 , GLY A:311 , 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 , ASN A:421 , GLY A:446 , GLY A:465 , ASN A:466 , ASN A:467 , TTN A:603 , HOH A:4006
BINDING SITE FOR RESIDUE NAD A 601
06
AC6
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 , ASP D:244 , ARG D:245
BINDING SITE FOR RESIDUE NAD A 602
07
AC7
SOFTWARE
ARG B:165 , LEU B:167 , GLY B:168 , ASN B:259 , THR B:283 , LEU B:310 , GLY B:311 , ALA B:312 , GLY B:313 , GLU B:314 , ALA B:315 , ASP B:345 , LYS B:346 , VAL B:392 , ALA B:393 , GLY B:394 , ALA B:395 , LEU B:419 , SER B:420 , ASN B:421 , GLY B:446 , GLY B:465 , ASN B:466 , ASN B:467 , TTN B:1603 , HOH B:4018
BINDING SITE FOR RESIDUE NAD B 1601
08
AC8
SOFTWARE
HIS B:154 , LYS B:156 , GLY B:192 , ILE B:193 , ARG B:194 , ARG B:197 , LEU B:480 , ARG B:542 , TYR B:552 , ARG B:556 , HOH B:4069 , ARG C:245 , HOH C:4090
BINDING SITE FOR RESIDUE NAD B 1602
09
AC9
SOFTWARE
ARG C:165 , LEU C:167 , GLY C:168 , ASN C:259 , THR C:283 , GLY C:311 , ALA C:312 , GLY C:313 , GLU C:314 , ALA C:315 , ASP C:345 , LYS C:346 , VAL C:392 , ALA C:393 , GLY C:394 , ALA C:395 , LEU C:419 , SER C:420 , ASN C:421 , GLY C:446 , GLY C:465 , ASN C:466 , ASN C:467 , TTN C:2603 , HOH C:4002
BINDING SITE FOR RESIDUE NAD C 2601
10
BC1
SOFTWARE
ASP B:244 , ARG B:245 , LYS C:156 , GLY C:192 , ILE C:193 , ARG C:194 , ILE C:479 , LEU C:480 , ASN C:482 , ARG C:542 , TYR C:552 , ARG C:556 , HOH C:4060
BINDING SITE FOR RESIDUE NAD C 2602
11
BC2
SOFTWARE
ARG D:165 , LEU D:167 , GLY D:168 , ASN D:259 , ASP D:279 , THR D:283 , GLY D:311 , ALA D:312 , GLY D:313 , GLU D:314 , ALA D:315 , ASP D:345 , LYS D:346 , VAL D:392 , ALA D:393 , GLY D:394 , ALA D:395 , LEU D:398 , LEU D:419 , ASN D:421 , GLY D:446 , GLY D:465 , ASN D:466 , ASN D:467 , TTN D:3603 , HOH D:4041
BINDING SITE FOR RESIDUE NAD D 3601
12
BC3
SOFTWARE
ASP A:244 , ARG A:245 , HIS D:154 , GLY D:192 , ILE D:193 , ARG D:194 , ARG D:197 , ILE D:479 , LEU D:480 , ASN D:482 , ARG D:542 , TYR D:552 , ARG D:556
BINDING SITE FOR RESIDUE NAD D 3602
13
BC4
SOFTWARE
TYR A:112 , ARG A:165 , LEU A:167 , LYS A:183 , GLU A:255 , ASP A:256 , ASP A:279 , ASN A:421 , ASN A:467 , NAD A:601 , MG A:604
BINDING SITE FOR RESIDUE TTN A 603
14
BC5
SOFTWARE
TYR B:112 , ARG B:165 , LEU B:167 , LYS B:183 , GLU B:255 , ASP B:256 , ASP B:279 , ASN B:421 , ASN B:467 , NAD B:1601 , MG B:1604
BINDING SITE FOR RESIDUE TTN B 1603
15
BC6
SOFTWARE
TYR C:112 , ARG C:165 , LEU C:167 , LYS C:183 , GLU C:255 , ASP C:256 , ASP C:279 , ASN C:421 , ASN C:467 , NAD C:2601 , MG C:2604
BINDING SITE FOR RESIDUE TTN C 2603
16
BC7
SOFTWARE
TYR D:112 , ARG D:165 , LEU D:167 , LYS D:183 , GLU D:255 , ASP D:256 , ASP D:279 , ASN D:421 , ASN D:467 , NAD D:3601 , MG D:3604
BINDING SITE FOR RESIDUE TTN D 3603
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_034104 (P114L, chain A/B/C/D, )
2: VAR_050017 (G450E, chain 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
P
114
L
2
UniProt
VAR_050017
G
450
E
MAOM_HUMAN
Polymorphism
649224
A/B/C/D
G
450
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:276-292,C:276-292,D:27...)
;
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:276-292
C:276-292
D:276-292
[
close PROSITE info
]
Exons
(15, 60)
Info
All Exons
Exon 1.2 (A:21-36 | B:21-36 | C:21-36 | D:21...)
Exon 1.3 (A:37-81 | B:37-81 | C:37-81 | D:37...)
Exon 1.4 (A:81-131 | B:81-131 | C:81-131 | D...)
Exon 1.5 (A:131-156 | B:131-156 | C:131-156 ...)
Exon 1.6 (A:157-210 | B:157-210 | C:157-210 ...)
Exon 1.7 (A:211-245 | B:211-245 | C:211-245 ...)
Exon 1.8 (A:245-282 | B:245-282 | C:245-282 ...)
Exon 1.9 (A:282-314 | B:282-314 | C:282-314 ...)
Exon 1.10 (A:315-352 | B:315-352 | C:315-352 ...)
Exon 1.11 (A:353-391 | B:353-391 | C:353-391 ...)
Exon 1.12 (A:391-438 | B:391-438 | C:391-438 ...)
Exon 1.13 (A:439-473 | B:439-473 | C:439-473 ...)
Exon 1.14 (A:473-496 | B:473-496 | C:473-496 ...)
Exon 1.15 (A:497-529 | B:497-529 | C:497-529 ...)
Exon 1.16b (A:530-573 | B:530-573 | C:530-573 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16b
16: Boundary 1.16b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000321341
1a
ENSE00001948888
chr18:
48405419-48405678
260
MAOM_HUMAN
-
0
0
-
-
1.2
ENST00000321341
2
ENSE00001222938
chr18:
48422179-48422298
120
MAOM_HUMAN
1-36
36
4
A:21-36
B:21-36
C:21-36
D:21-36
16
16
16
16
1.3
ENST00000321341
3
ENSE00000996845
chr18:
48434433-48434566
134
MAOM_HUMAN
37-81
45
4
A:37-81
B:37-81
C:37-81
D:37-81
45
45
45
45
1.4
ENST00000321341
4
ENSE00000996846
chr18:
48439171-48439320
150
MAOM_HUMAN
81-131
51
4
A:81-131
B:81-131
C:81-131
D:81-131
51
51
51
51
1.5
ENST00000321341
5
ENSE00001151659
chr18:
48442538-48442613
76
MAOM_HUMAN
131-156
26
4
A:131-156
B:131-156
C:131-156
D:131-156
26
26
26
26
1.6
ENST00000321341
6
ENSE00001151654
chr18:
48443717-48443878
162
MAOM_HUMAN
157-210
54
4
A:157-210
B:157-210
C:157-210
D:157-210
54
54
54
54
1.7
ENST00000321341
7
ENSE00001151650
chr18:
48444480-48444583
104
MAOM_HUMAN
211-245
35
4
A:211-245
B:211-245
C:211-245
D:211-245
35
35
35
35
1.8
ENST00000321341
8
ENSE00001151645
chr18:
48446826-48446935
110
MAOM_HUMAN
245-282
38
4
A:245-282
B:245-282
C:245-282
D:245-282
38
38
38
38
1.9
ENST00000321341
9
ENSE00001151639
chr18:
48447031-48447128
98
MAOM_HUMAN
282-314
33
4
A:282-314
B:282-314
C:282-314
D:282-314
33
33
33
33
1.10
ENST00000321341
10
ENSE00001151634
chr18:
48447444-48447557
114
MAOM_HUMAN
315-352
38
4
A:315-352
B:315-352
C:315-352
D:315-352
38
38
38
38
1.11
ENST00000321341
11
ENSE00000950181
chr18:
48450468-48450582
115
MAOM_HUMAN
353-391
39
4
A:353-391
B:353-391
C:353-391
D:353-391
39
39
39
39
1.12
ENST00000321341
12
ENSE00000950182
chr18:
48452126-48452268
143
MAOM_HUMAN
391-438
48
4
A:391-438
B:391-438
C:391-438
D:391-438
48
48
48
48
1.13
ENST00000321341
13
ENSE00000950183
chr18:
48458628-48458730
103
MAOM_HUMAN
439-473
35
4
A:439-473
B:439-473
C:439-473
D:439-473
35
35
35
35
1.14
ENST00000321341
14
ENSE00000950184
chr18:
48465940-48466010
71
MAOM_HUMAN
473-496
24
4
A:473-496
B:473-496
C:473-496
D:473-496
24
24
24
24
1.15
ENST00000321341
15
ENSE00000950185
chr18:
48466658-48466756
99
MAOM_HUMAN
497-529
33
4
A:497-529
B:497-529
C:497-529
D:497-529
33
33
33
33
1.16b
ENST00000321341
16b
ENSE00001605064
chr18:
48473387-48474691
1305
MAOM_HUMAN
530-584
55
4
A:530-573
B:530-573
C:530-573
D:530-573
44
44
44
44
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1efla2 (A:21-279)
1b: SCOP_d1eflb2 (B:21-279)
1c: SCOP_d1eflc2 (C:21-279)
1d: SCOP_d1efld2 (D:21-279)
2a: SCOP_d1efla1 (A:280-573)
2b: SCOP_d1eflb1 (B:280-573)
2c: SCOP_d1eflc1 (C:280-573)
2d: SCOP_d1efld1 (D:280-573)
View:
Select:
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
d1efla2
A:21-279
1b
d1eflb2
B:21-279
1c
d1eflc2
C:21-279
1d
d1efld2
D:21-279
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
d1efla1
A:280-573
2b
d1eflb1
B:280-573
2c
d1eflc1
C:280-573
2d
d1efld1
D:280-573
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1eflA01 (A:21-277)
1b: CATH_1eflB01 (B:21-277)
1c: CATH_1eflC01 (C:21-277)
1d: CATH_1eflD01 (D:21-277)
2a: CATH_1eflA02 (A:278-573)
2b: CATH_1eflB02 (B:278-573)
2c: CATH_1eflC02 (C:278-573)
2d: CATH_1eflD02 (D:278-573)
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
1eflA01
A:21-277
1b
1eflB01
B:21-277
1c
1eflC01
C:21-277
1d
1eflD01
D:21-277
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1eflA02
A:278-573
2b
1eflB02
B:278-573
2c
1eflC02
C:278-573
2d
1eflD02
D:278-573
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
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RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
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Show PDB file:
Asym.Unit (375 KB)
Header - Asym.Unit
Biol.Unit 1 (362 KB)
Header - Biol.Unit 1
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