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1G0R
Asym. Unit
Info
Asym.Unit (873 KB)
Biol.Unit 1 (439 KB)
Biol.Unit 2 (433 KB)
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Title
:
THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). THYMIDINE/GLUCOSE-1-PHOSPHATE COMPLEX.
Authors
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
Date
:
07 Oct 00 (Deposition) - 27 Dec 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.87
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
:
L-Rhamnose, Nucleotidyltransferase, Pyrophosphorylase, Thymidylyltransferase, Allostery, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
The Structural Basis Of The Catalytic Mechanism And Regulation Of Glucose-1-Phosphate Thymidylyltransferase (Rmla).
Embo J. V. 19 6652 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 46)
Info
All Hetero Components
1a: ALPHA-D-GLUCOSE-1-PHOSPHATE (G1Pa)
1b: ALPHA-D-GLUCOSE-1-PHOSPHATE (G1Pb)
1c: ALPHA-D-GLUCOSE-1-PHOSPHATE (G1Pc)
1d: ALPHA-D-GLUCOSE-1-PHOSPHATE (G1Pd)
1e: ALPHA-D-GLUCOSE-1-PHOSPHATE (G1Pe)
1f: ALPHA-D-GLUCOSE-1-PHOSPHATE (G1Pf)
1g: ALPHA-D-GLUCOSE-1-PHOSPHATE (G1Pg)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
3a: THYMIDINE (THMa)
3b: THYMIDINE (THMb)
3c: THYMIDINE (THMc)
3d: THYMIDINE (THMd)
3e: THYMIDINE (THMe)
3f: THYMIDINE (THMf)
3g: THYMIDINE (THMg)
3h: THYMIDINE (THMh)
3i: THYMIDINE (THMi)
3j: THYMIDINE (THMj)
3k: THYMIDINE (THMk)
3l: THYMIDINE (THMl)
3m: THYMIDINE (THMm)
3n: THYMIDINE (THMn)
3o: THYMIDINE (THMo)
3p: THYMIDINE (THMp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G1P
7
Ligand/Ion
ALPHA-D-GLUCOSE-1-PHOSPHATE
2
SO4
23
Ligand/Ion
SULFATE ION
3
THM
16
Ligand/Ion
THYMIDINE
[
close Hetero Component info
]
Sites
(46, 46)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:88 , LEU A:108 , ASN A:111 , TYR A:145 , GLY A:146 , GLU A:161 , LYS A:162 , VAL A:172 , THR A:200 , TRP A:223 , THM A:2530 , HOH A:2564 , HOH A:2623 , HOH A:2688 , HOH A:2818
BINDING SITE FOR RESIDUE G1P A 2500
02
AC2
SOFTWARE
LEU B:88 , ASN B:111 , TYR B:145 , GLY B:146 , GLU B:161 , LYS B:162 , VAL B:172 , THM B:2531 , HOH B:2608 , HOH B:2627 , HOH B:2846
BINDING SITE FOR RESIDUE G1P B 2501
03
AC3
SOFTWARE
ASN C:111 , TYR C:145 , GLY C:146 , GLU C:161 , LYS C:162 , VAL C:172 , ARG C:194 , THR C:200 , TRP C:223 , THM C:2532 , HOH C:2615 , HOH C:2812
BINDING SITE FOR RESIDUE G1P C 2502
04
AC4
SOFTWARE
LEU D:88 , LEU D:108 , ASN D:111 , TYR D:145 , GLY D:146 , GLU D:161 , LYS D:162 , VAL D:172 , TRP D:223 , THM D:2533 , HOH D:2562
BINDING SITE FOR RESIDUE G1P D 2503
05
AC5
SOFTWARE
LEU E:88 , LEU E:108 , ASN E:111 , TYR E:145 , GLY E:146 , GLU E:161 , LYS E:162 , VAL E:172 , THR E:200 , TRP E:223 , THM E:2534 , HOH E:2571
BINDING SITE FOR RESIDUE G1P E 2504
06
AC6
SOFTWARE
LEU G:88 , LEU G:108 , ASN G:111 , TYR G:145 , GLY G:146 , GLU G:161 , LYS G:162 , VAL G:172 , THM G:2536 , HOH G:2572 , HOH G:2685 , HOH G:2689 , HOH G:2870
BINDING SITE FOR RESIDUE G1P G 2505
07
AC7
SOFTWARE
LEU H:88 , ASN H:111 , TYR H:145 , GLY H:146 , GLU H:161 , LYS H:162 , VAL H:172 , TRP H:223 , ASP H:225 , THM H:2537 , HOH H:2570 , HOH H:2769 , HOH H:2827 , HOH H:2828 , HOH H:2829
BINDING SITE FOR RESIDUE G1P H 2506
08
AC8
SOFTWARE
SER A:12 , GLY A:13 , THR A:14 , ARG A:15 , HOH A:2728 , HOH A:2824
BINDING SITE FOR RESIDUE SO4 A 2507
09
AC9
SOFTWARE
HIS A:116 , ASP A:117 , THM A:2538 , HOH A:2592 , HOH A:2621 , HOH A:2749 , HOH A:2782 , HOH A:2806 , GLY C:218 , ARG C:219 , GLY C:220
BINDING SITE FOR RESIDUE SO4 A 2508
10
BC1
SOFTWARE
ASP C:151 , GLN C:152 , HOH C:2620 , HOH C:2745 , ARG G:128 , GLU G:215 , HOH G:2613
BINDING SITE FOR RESIDUE SO4 C 2509
11
BC2
SOFTWARE
SER B:12 , GLY B:13 , THR B:14 , ARG B:15 , LYS B:25 , HOH B:2813
BINDING SITE FOR RESIDUE SO4 B 2510
12
BC3
SOFTWARE
HIS B:116 , ASP B:117 , THM B:2539 , HOH B:2588 , HOH B:2698 , HOH B:2705 , HOH B:2772 , HOH B:2776 , GLY D:218 , ARG D:219 , GLY D:220
BINDING SITE FOR RESIDUE SO4 B 2511
13
BC4
SOFTWARE
ASP D:151 , GLN D:152 , HOH D:2614 , HOH D:2725 , HOH D:2798 , ARG H:128 , GLU H:215 , HOH H:2623
BINDING SITE FOR RESIDUE SO4 D 2512
14
BC5
SOFTWARE
GLY A:218 , ARG A:219 , GLY A:220 , HIS C:116 , ASP C:117 , THM C:2540 , HOH C:2566 , HOH C:2609 , HOH C:2685 , HOH C:2776
BINDING SITE FOR RESIDUE SO4 C 2513
15
BC6
SOFTWARE
ARG C:62 , ARG D:62 , HOH D:2638
BINDING SITE FOR RESIDUE SO4 D 2514
16
BC7
SOFTWARE
ARG C:128 , GLN C:129 , THR C:130
BINDING SITE FOR RESIDUE SO4 C 2515
17
BC8
SOFTWARE
GLY B:218 , ARG B:219 , GLY B:220 , HIS D:116 , ASP D:117 , THM D:2541 , HOH D:2558 , HOH D:2598 , HOH D:2635 , HOH D:2705
BINDING SITE FOR RESIDUE SO4 D 2516
18
BC9
SOFTWARE
GLN D:127 , ARG D:128 , GLN D:129 , THR D:130
BINDING SITE FOR RESIDUE SO4 D 2517
19
CC1
SOFTWARE
HIS E:116 , ASP E:117 , THM E:2542 , GLY H:218 , ARG H:219 , GLY H:220 , HOH H:2620 , HOH H:2671
BINDING SITE FOR RESIDUE SO4 H 2518
20
CC2
SOFTWARE
ARG E:62 , ARG F:62 , HOH F:2735 , HOH F:2798
BINDING SITE FOR RESIDUE SO4 F 2519
21
CC3
SOFTWARE
GLN E:127 , ARG E:128 , GLN E:129 , THR E:130
BINDING SITE FOR RESIDUE SO4 E 2520
22
CC4
SOFTWARE
HIS F:116 , ASP F:117 , THM F:2543 , HOH F:2555 , HOH F:2731 , HOH F:2736 , HOH F:2778 , GLY G:218 , ARG G:219 , GLY G:220
BINDING SITE FOR RESIDUE SO4 F 2521
23
CC5
SOFTWARE
GLN F:127 , ARG F:128 , GLN F:129 , THR F:130
BINDING SITE FOR RESIDUE SO4 F 2522
24
CC6
SOFTWARE
GLY F:218 , ARG F:219 , GLY F:220 , HIS G:116 , ASP G:117 , THM G:2544 , HOH G:2578 , HOH G:2690 , HOH G:2733 , HOH G:2805
BINDING SITE FOR RESIDUE SO4 G 2523
25
CC7
SOFTWARE
ARG A:128 , GLU A:215 , HOH A:2690 , HOH A:2775 , ASP F:151 , GLN F:152 , HOH F:2719 , HOH F:2784
BINDING SITE FOR RESIDUE SO4 F 2524
26
CC8
SOFTWARE
GLU G:160 , GLU G:161 , ARG G:194 , ARG G:204 , HOH G:2643 , HOH G:2707 , HOH G:2742
BINDING SITE FOR RESIDUE SO4 G 2525
27
CC9
SOFTWARE
GLY H:11 , SER H:12 , GLY H:13 , LYS H:25 , THM H:2537 , HOH H:2628 , HOH H:2680 , HOH H:2826
BINDING SITE FOR RESIDUE SO4 H 2526
28
DC1
SOFTWARE
GLY E:218 , ARG E:219 , GLY E:220 , HIS H:116 , ASP H:117 , THM H:2545 , HOH H:2595 , HOH H:2763
BINDING SITE FOR RESIDUE SO4 E 2527
29
DC2
SOFTWARE
ARG B:128 , GLU B:215 , HOH B:2606 , HOH B:2723 , ASP E:151 , GLN E:152
BINDING SITE FOR RESIDUE SO4 B 2528
30
DC3
SOFTWARE
GLU H:160 , GLU H:161 , ARG H:204 , HOH H:2625
BINDING SITE FOR RESIDUE SO4 H 2529
31
DC4
SOFTWARE
LEU A:8 , GLY A:10 , GLY A:11 , GLN A:26 , GLN A:82 , PRO A:85 , ASP A:86 , GLY A:87 , LEU A:88 , GLY A:109 , ASP A:110 , G1P A:2500 , HOH A:2824
BINDING SITE FOR RESIDUE THM A 2530
32
DC5
SOFTWARE
LEU B:8 , GLY B:10 , GLY B:11 , GLN B:26 , GLN B:82 , PRO B:85 , ASP B:86 , GLY B:87 , GLY B:109 , ASP B:110 , GLU B:196 , G1P B:2501
BINDING SITE FOR RESIDUE THM B 2531
33
DC6
SOFTWARE
LEU C:8 , GLY C:10 , GLY C:11 , GLN C:26 , GLN C:82 , PRO C:85 , ASP C:86 , GLY C:87 , LEU C:88 , GLY C:109 , ASP C:110 , G1P C:2502
BINDING SITE FOR RESIDUE THM C 2532
34
DC7
SOFTWARE
LEU D:8 , ALA D:9 , GLY D:10 , GLY D:11 , GLN D:26 , GLN D:82 , PRO D:85 , ASP D:86 , GLY D:87 , LEU D:88 , GLY D:109 , ASP D:110 , G1P D:2503
BINDING SITE FOR RESIDUE THM D 2533
35
DC8
SOFTWARE
LEU E:8 , GLY E:10 , GLY E:11 , GLN E:26 , GLN E:82 , PRO E:85 , ASP E:86 , GLY E:87 , LEU E:88 , ASP E:110 , G1P E:2504
BINDING SITE FOR RESIDUE THM E 2534
36
DC9
SOFTWARE
LEU F:8 , GLY F:10 , GLY F:11 , LYS F:25 , GLN F:26 , GLN F:82 , PRO F:85 , ASP F:86 , GLY F:87 , LEU F:88 , GLY F:109 , ASP F:110
BINDING SITE FOR RESIDUE THM F 2535
37
EC1
SOFTWARE
LEU G:8 , GLY G:10 , GLY G:11 , GLN G:26 , GLN G:82 , PRO G:85 , ASP G:86 , GLY G:87 , LEU G:88 , GLY G:109 , ASP G:110 , G1P G:2505 , HOH G:2685
BINDING SITE FOR RESIDUE THM G 2536
38
EC2
SOFTWARE
LEU H:8 , GLY H:10 , GLY H:11 , GLN H:26 , GLN H:82 , PRO H:85 , ASP H:86 , GLY H:87 , LEU H:88 , GLY H:109 , ASP H:110 , G1P H:2506 , SO4 H:2526
BINDING SITE FOR RESIDUE THM H 2537
39
EC3
SOFTWARE
LEU A:45 , TYR A:114 , GLY A:115 , VAL A:250 , ALA A:251 , GLU A:255 , ILE A:256 , ARG A:259 , SO4 A:2508 , HOH A:2558 , HOH A:2565 , HOH A:2581 , HOH A:2663 , ARG C:219 , GLY C:220
BINDING SITE FOR RESIDUE THM A 2538
40
EC4
SOFTWARE
LEU B:45 , TYR B:114 , GLY B:115 , VAL B:250 , ALA B:251 , GLU B:255 , ILE B:256 , SO4 B:2511 , HOH B:2558 , HOH B:2576 , HOH B:2751 , HOH B:2842 , ARG D:219 , GLY D:220
BINDING SITE FOR RESIDUE THM B 2539
41
EC5
SOFTWARE
ARG A:219 , LEU C:45 , TYR C:114 , GLY C:115 , VAL C:250 , ALA C:251 , GLU C:255 , ILE C:256 , ARG C:259 , SO4 C:2513 , HOH C:2542 , HOH C:2559 , HOH C:2584
BINDING SITE FOR RESIDUE THM C 2540
42
EC6
SOFTWARE
ARG B:219 , LEU D:45 , TYR D:114 , GLY D:115 , VAL D:250 , ALA D:251 , GLU D:255 , ILE D:256 , SO4 D:2516 , HOH D:2550 , HOH D:2568 , HOH D:2577 , HOH D:2685
BINDING SITE FOR RESIDUE THM D 2541
43
EC7
SOFTWARE
LEU E:45 , TYR E:114 , GLY E:115 , VAL E:250 , ALA E:251 , GLU E:255 , ILE E:256 , ARG E:259 , HOH E:2548 , HOH E:2555 , HOH E:2563 , HOH E:2707 , ARG H:219 , GLY H:220 , SO4 H:2518
BINDING SITE FOR RESIDUE THM E 2542
44
EC8
SOFTWARE
LEU F:45 , TYR F:114 , GLY F:115 , VAL F:250 , ALA F:251 , GLU F:255 , SO4 F:2521 , HOH F:2545 , HOH F:2613 , HOH F:2618 , ARG G:219
BINDING SITE FOR RESIDUE THM F 2543
45
EC9
SOFTWARE
ARG F:219 , GLY F:220 , LEU G:45 , TYR G:114 , GLY G:115 , VAL G:250 , ALA G:251 , GLU G:255 , ILE G:256 , ARG G:259 , SO4 G:2523 , HOH G:2559 , HOH G:2568 , HOH G:2592
BINDING SITE FOR RESIDUE THM G 2544
46
FC1
SOFTWARE
ARG E:219 , GLY E:220 , SO4 E:2527 , LEU H:45 , TYR H:114 , GLY H:115 , VAL H:250 , ALA H:251 , GLU H:255 , ILE H:256 , ARG H:259 , HOH H:2569 , HOH H:2572 , HOH H:2577
BINDING SITE FOR RESIDUE THM H 2545
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1g0ra_ (A:)
1b: SCOP_d1g0rb_ (B:)
1c: SCOP_d1g0rc_ (C:)
1d: SCOP_d1g0rd_ (D:)
1e: SCOP_d1g0re_ (E:)
1f: SCOP_d1g0rf_ (F:)
1g: SCOP_d1g0rg_ (G:)
1h: SCOP_d1g0rh_ (H:)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
glucose-1-phosphate thymidylyltransferase
(43)
Protein domain
:
RmlA (RfbA)
(27)
Pseudomonas aeruginosa [TaxId: 287]
(9)
1a
d1g0ra_
A:
1b
d1g0rb_
B:
1c
d1g0rc_
C:
1d
d1g0rd_
D:
1e
d1g0re_
E:
1f
d1g0rf_
F:
1g
d1g0rg_
G:
1h
d1g0rh_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1g0rA00 (A:2-293)
1b: CATH_1g0rB00 (B:2-293)
1c: CATH_1g0rC00 (C:2-293)
1d: CATH_1g0rD00 (D:2-293)
1e: CATH_1g0rE00 (E:2-293)
1f: CATH_1g0rG00 (G:2-293)
1g: CATH_1g0rH00 (H:2-293)
1h: CATH_1g0rF00 (F:1-293)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Pseudomonas aeruginosa. Organism_taxid: 287.
(7)
1a
1g0rA00
A:2-293
1b
1g0rB00
B:2-293
1c
1g0rC00
C:2-293
1d
1g0rD00
D:2-293
1e
1g0rE00
E:2-293
1f
1g0rG00
G:2-293
1g
1g0rH00
H:2-293
1h
1g0rF00
F:1-293
[
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Pfam Domains
(0, 0)
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all PFAM domains
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Atom Selection
(currently selected atoms:
all
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Asymmetric Unit 1
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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)
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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") .
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