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1SXJ
Asym. Unit
Info
Asym.Unit (382 KB)
Biol.Unit 1 (372 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE EUKARYOTIC CLAMP LOADER (REPLICATION FACTOR C, RFC) BOUND TO THE DNA SLIDING CLAMP (PROLIFERATING CELL NUCLEAR ANTIGEN, PCNA)
Authors
:
G. D. Bowman, M. O'Donnell, J. Kuriyan
Date
:
30 Mar 04 (Deposition) - 22 Jun 04 (Release) - 15 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Clamp Loader, Processivity Clamp, Dna Sliding Clamp, Aaa+ Atpase, Dna Polymerase, Dna-Binding Protein, Replication
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. D. Bowman, M. O'Donnell, J. Kuriyan
Structural Analysis Of A Eukaryotic Sliding Dna Clamp-Clamp Loader Complex.
Nature V. 429 724 2004
[
close entry info
]
Hetero Components
(5, 75)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSa)
2b: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSb)
2c: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSc)
2d: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLA... (AGSd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
5a: (UNKa)
5aa: (UNKaa)
5ab: (UNKab)
5ac: (UNKac)
5ad: (UNKad)
5ae: (UNKae)
5af: (UNKaf)
5ag: (UNKag)
5ah: (UNKah)
5ai: (UNKai)
5aj: (UNKaj)
5ak: (UNKak)
5al: (UNKal)
5am: (UNKam)
5an: (UNKan)
5ao: (UNKao)
5ap: (UNKap)
5aq: (UNKaq)
5ar: (UNKar)
5as: (UNKas)
5at: (UNKat)
5b: (UNKb)
5c: (UNKc)
5d: (UNKd)
5e: (UNKe)
5f: (UNKf)
5g: (UNKg)
5h: (UNKh)
5i: (UNKi)
5j: (UNKj)
5k: (UNKk)
5l: (UNKl)
5m: (UNKm)
5n: (UNKn)
5o: (UNKo)
5p: (UNKp)
5q: (UNKq)
5r: (UNKr)
5s: (UNKs)
5t: (UNKt)
5u: (UNKu)
5v: (UNKv)
5w: (UNKw)
5x: (UNKx)
5y: (UNKy)
5z: (UNKz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
AGS
4
Ligand/Ion
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
5
UNK
46
Mod. Amino Acid
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:360 , AGS A:801
BINDING SITE FOR RESIDUE MG A 811
2
AC2
SOFTWARE
THR B:56 , ASP B:114 , AGS B:802 , ARG C:131
BINDING SITE FOR RESIDUE MG B 812
3
AC3
SOFTWARE
THR C:60 , ASP C:117 , AGS C:803
BINDING SITE FOR RESIDUE MG C 813
4
AC4
SOFTWARE
THR D:72 , ASP D:140 , GLU D:141 , AGS D:804 , ARG E:155
BINDING SITE FOR RESIDUE MG D 814
5
AC5
SOFTWARE
THR A:299 , TYR A:302 , ALA A:303 , PRO A:304 , GLN A:309 , VAL A:310 , CYS A:311 , GLY A:356 , ILE A:357 , GLY A:358 , LYS A:359 , THR A:360 , THR A:361 , ASN A:456 , ILE A:514 , ARG A:515 , MG A:811 , ARG B:128 , GLU B:132
BINDING SITE FOR RESIDUE AGS A 801
6
AC6
SOFTWARE
VAL B:12 , TYR B:15 , ARG B:16 , PRO B:17 , ILE B:23 , VAL B:24 , GLY B:25 , GLY B:52 , ILE B:53 , GLY B:54 , LYS B:55 , THR B:56 , THR B:57 , ASN B:145 , ARG B:174 , MET B:202 , ARG B:203 , MG B:812 , ARG C:131 , ALA C:156
BINDING SITE FOR RESIDUE AGS B 802
7
AC7
SOFTWARE
VAL C:16 , TYR C:19 , ARG C:20 , PRO C:21 , VAL C:27 , TYR C:28 , PRO C:55 , GLY C:56 , THR C:57 , GLY C:58 , LYS C:59 , THR C:60 , SER C:61 , ASN C:148 , LEU C:169 , MET C:205 , ARG C:206 , LEU C:209 , MG C:813 , ARG D:154
BINDING SITE FOR RESIDUE AGS C 803
8
AC8
SOFTWARE
VAL D:28 , GLU D:29 , TYR D:31 , ARG D:32 , PRO D:33 , VAL D:39 , THR D:40 , ALA D:41 , PRO D:67 , GLY D:68 , THR D:69 , GLY D:70 , LYS D:71 , THR D:72 , SER D:73 , ASN D:171 , LEU D:228 , ARG D:229 , MG D:814 , ARG E:155 , PRO E:180
BINDING SITE FOR RESIDUE AGS D 804
9
AC9
SOFTWARE
VAL E:5 , ARG E:9 , PRO E:10 , SER E:17 , HIS E:18 , PRO E:44 , ASN E:45 , GLY E:46 , THR E:47 , GLY E:48 , LYS E:49 , LYS E:50 , THR E:51 , ILE E:201 , LEU E:230 , ARG E:231 , LEU E:234
BINDING SITE FOR RESIDUE ADP E 805
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PCNA_1 (F:34-57,G:34-57,H:34-57)
2: PCNA_2 (F:61-79,G:61-79,H:61-79)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PCNA_1
PS01251
Proliferating cell nuclear antigen signature 1.
PCNA_YEAST
34-57
3
F:34-57
G:34-57
H:34-57
2
PCNA_2
PS00293
Proliferating cell nuclear antigen signature 2.
PCNA_YEAST
61-79
3
F:61-79
G:61-79
H:61-79
[
close PROSITE info
]
Exons
(6, 8)
Info
All Exons
Exon 1.1 (E:4-354 (gaps))
Exon 2.1 (F:1-256 | G:1-255 | H:1-254)
Exon 3.1 (D:26-353)
Exon 4.1 (C:12-333)
Exon 5.1 (B:7-322)
Exon 6.1 (A:295-747 (gaps))
View:
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All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/-
03: Boundary -/2.1
04: Boundary 2.1/-
05: Boundary -/3.1
06: Boundary 3.1/-
07: Boundary -/4.1
08: Boundary 4.1/-
09: Boundary -/5.1
10: Boundary 5.1/-
11: Boundary -/6.1
12: Boundary 6.1/-
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
1.1
YBR087W
1
YBR087W.1
II:423759-424823
1065
RFC5_YEAST
1-354
354
1
E:4-354 (gaps)
351
2.1
YBR088C
1
YBR088C.1
II:425760-424984
777
PCNA_YEAST
1-258
258
3
F:1-256
G:1-255
H:1-254
256
255
254
3.1
YJR068W
1
YJR068W.1
X:567635-568696
1062
RFC2_YEAST
1-353
353
1
D:26-353
328
4.1
YNL290W
1
YNL290W.1
XIV:86218-87240
1023
RFC3_YEAST
1-340
340
1
C:12-333
322
5.1
YOL094C
1
YOL094C.1
XV:142555-141584
972
RFC4_YEAST
1-323
323
1
B:7-322
316
6.1
YOR217W
1
YOR217W.1
XV:749302-751887
2586
RFC1_YEAST
1-861
861
1
A:295-747 (gaps)
453
[
close EXON info
]
SCOP Domains
(11, 16)
Info
All SCOP Domains
01a: SCOP_d1sxja1 (A:548-693)
02a: SCOP_d1sxjd1 (D:263-353)
03a: SCOP_d1sxjc1 (C:239-333)
04a: SCOP_d1sxjb1 (B:231-322)
05a: SCOP_d1sxje1 (E:256-354)
06a: SCOP_d1sxjf1 (F:1-126)
06b: SCOP_d1sxjf2 (F:127-256)
06c: SCOP_d1sxjg1 (G:1-126)
06d: SCOP_d1sxjg2 (G:127-255)
06e: SCOP_d1sxjh1 (H:1-126)
06f: SCOP_d1sxjh2 (H:127-254)
07a: SCOP_d1sxja2 (A:295-547)
08a: SCOP_d1sxjd2 (D:26-262)
09a: SCOP_d1sxjc2 (C:12-238)
10a: SCOP_d1sxjb2 (B:7-230)
11a: SCOP_d1sxje2 (E:4-255)
View:
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Classes
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Folds
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Superfamilies
(
)
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Families
(
)
(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
post-AAA+ oligomerization domain-like
(22)
Superfamily
:
post-AAA+ oligomerization domain-like
(22)
Family
:
DNA polymerase III clamp loader subunits, C-terminal domain
(18)
Protein domain
:
Replication factor C1
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
01a
d1sxja1
A:548-693
Protein domain
:
Replication factor C2
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
02a
d1sxjd1
D:263-353
Protein domain
:
Replication factor C3
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
03a
d1sxjc1
C:239-333
Protein domain
:
Replication factor C4
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
04a
d1sxjb1
B:231-322
Protein domain
:
Replication factor C5
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
05a
d1sxje1
E:256-354
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNA clamp
(88)
Superfamily
:
DNA clamp
(88)
Family
:
DNA polymerase processivity factor
(40)
Protein domain
:
Proliferating cell nuclear antigen (PCNA)
(24)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(6)
06a
d1sxjf1
F:1-126
06b
d1sxjf2
F:127-256
06c
d1sxjg1
G:1-126
06d
d1sxjg2
G:127-255
06e
d1sxjh1
H:1-126
06f
d1sxjh2
H:127-254
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Extended AAA-ATPase domain
(92)
Protein domain
:
Replication factor C1
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
07a
d1sxja2
A:295-547
Protein domain
:
Replication factor C2
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
08a
d1sxjd2
D:26-262
Protein domain
:
Replication factor C3
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
09a
d1sxjc2
C:12-238
Protein domain
:
Replication factor C4
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
10a
d1sxjb2
B:7-230
Protein domain
:
Replication factor C5
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
11a
d1sxje2
E:4-255
[
close SCOP info
]
CATH Domains
(5, 16)
Info
all CATH domains
1a: CATH_1sxjD01 (D:26-192)
1b: CATH_1sxjE01 (E:4-193)
1c: CATH_1sxjB01 (B:7-166)
1d: CATH_1sxjC01 (C:12-169)
2a: CATH_1sxjG00 (G:-1-255)
2b: CATH_1sxjF00 (F:-1-256)
3a: CATH_1sxjH02 (H:127-254)
4a: CATH_1sxjB02 (B:167-230)
4b: CATH_1sxjD02 (D:193-262)
4c: CATH_1sxjC02 (C:170-238)
4d: CATH_1sxjE02 (E:194-257)
5a: CATH_1sxjE03 (E:258-354)
5b: CATH_1sxjC03 (C:239-333)
5c: CATH_1sxjA03 (A:550-666)
5d: CATH_1sxjB03 (B:231-322)
5e: CATH_1sxjD03 (D:263-353)
View:
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Architectures
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Baker's yeast (Saccharomyces cerevisiae)
(61)
1a
1sxjD01
D:26-192
1b
1sxjE01
E:4-193
1c
1sxjB01
B:7-166
1d
1sxjC01
C:12-169
Architecture
:
Box
(41)
Topology
:
Proliferating Cell Nuclear Antigen
(41)
Homologous Superfamily
:
[code=3.70.10.10, no name defined]
(41)
Baker's yeast (Saccharomyces cerevisiae)
(4)
2a
1sxjG00
G:-1-255
2b
1sxjF00
F:-1-256
Architecture
:
Roll
(3276)
Topology
:
DNA Polymerase III; Chain A, domain 2
(13)
Homologous Superfamily
:
DNA Polymerase III, subunit A, domain 2
(13)
Baker's yeast (Saccharomyces cerevisiae)
(1)
3a
1sxjH02
H:127-254
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helicase, Ruva Protein; domain 3
(218)
Homologous Superfamily
:
[code=1.10.8.60, no name defined]
(73)
Baker's yeast (Saccharomyces cerevisiae)
(1)
4a
1sxjB02
B:167-230
4b
1sxjD02
D:193-262
4c
1sxjC02
C:170-238
4d
1sxjE02
E:194-257
Architecture
:
Up-down Bundle
(3216)
Topology
:
Zinc Finger, Delta Prime; domain 3
(17)
Homologous Superfamily
:
[code=1.20.272.10, no name defined]
(16)
Baker's yeast (Saccharomyces cerevisiae)
(1)
5a
1sxjE03
E:258-354
5b
1sxjC03
C:239-333
5c
1sxjA03
A:550-666
5d
1sxjB03
B:231-322
5e
1sxjD03
D:263-353
[
close CATH info
]
Pfam Domains
(6, 16)
Info
all PFAM domains
1a: PFAM_PCNA_C_1sxjH01 (H:127-254)
1b: PFAM_PCNA_C_1sxjH02 (H:127-254)
1c: PFAM_PCNA_C_1sxjH03 (H:127-254)
2a: PFAM_PCNA_N_1sxjH04 (H:1-126)
2b: PFAM_PCNA_N_1sxjH05 (H:1-126)
2c: PFAM_PCNA_N_1sxjH06 (H:1-126)
3a: PFAM_AAA_1sxjA01 (A:349-478)
3b: PFAM_AAA_1sxjD01 (D:61-192)
3c: PFAM_AAA_1sxjC01 (C:49-169)
3d: PFAM_AAA_1sxjB01 (B:45-166)
4a: PFAM_DNA_pol3_delta2_1sxjE01 (E:18-194)
5a: PFAM_RFC1_1sxjA02 (A:621-747)
6a: PFAM_Rep_fac_C_1sxjD02 (D:261-350)
6b: PFAM_Rep_fac_C_1sxjC02 (C:237-327)
6c: PFAM_Rep_fac_C_1sxjB02 (B:229-316)
6d: PFAM_Rep_fac_C_1sxjE02 (E:258-349)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
DNA_clamp
(33)
Family
:
PCNA_C
(23)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(6)
1a
PCNA_C-1sxjH01
H:127-254
1b
PCNA_C-1sxjH02
H:127-254
1c
PCNA_C-1sxjH03
H:127-254
Family
:
PCNA_N
(25)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(8)
2a
PCNA_N-1sxjH04
H:1-126
2b
PCNA_N-1sxjH05
H:1-126
2c
PCNA_N-1sxjH06
H:1-126
Clan
:
P-loop_NTPase
(1112)
Family
:
AAA
(26)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(4)
3a
AAA-1sxjA01
A:349-478
3b
AAA-1sxjD01
D:61-192
3c
AAA-1sxjC01
C:49-169
3d
AAA-1sxjB01
B:45-166
Family
:
DNA_pol3_delta2
(6)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
4a
DNA_pol3_delta2-1sxjE01
E:18-194
Clan
:
no clan defined [family: RFC1]
(1)
Family
:
RFC1
(1)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
5a
RFC1-1sxjA02
A:621-747
Clan
:
no clan defined [family: Rep_fac_C]
(1)
Family
:
Rep_fac_C
(1)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
6a
Rep_fac_C-1sxjD02
D:261-350
6b
Rep_fac_C-1sxjC02
C:237-327
6c
Rep_fac_C-1sxjB02
B:229-316
6d
Rep_fac_C-1sxjE02
E:258-349
[
close Pfam info
]
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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)
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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") .
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