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3KQX
Biol. Unit 2
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (519 KB)
Biol.Unit 2 (520 KB)
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(1)
Title
:
STRUCTURE OF A PROTEASE 1
Authors
:
S. Mcgowan, J. C. Whisstock
Date
:
17 Nov 09 (Deposition) - 02 Feb 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.01
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Protease, Aminopeptidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Mcgowan, C. A. Oellig, W. A. Birru, T. T. Caradoc-Davies, C. M. Stack J. Lowther, T. Skinner-Adams, A. Mucha, P. Kafarski, J. Grembecka, K. R. Trenholme, A. M. Buckle, D. L. Gardiner, J. P. Dalton, J. C. Whisstock
Structure Of The Plasmodium Falciparum M17 Aminopeptidase And Significance For The Design Of Drugs Targeting The Neutral Exopeptidases
Proc. Natl. Acad. Sci. Usa V. 107 2449 2010
[
close entry info
]
Hetero Components
(4, 42)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1aa: PENTAETHYLENE GLYCOL (1PEaa)
1ab: PENTAETHYLENE GLYCOL (1PEab)
1ac: PENTAETHYLENE GLYCOL (1PEac)
1ad: PENTAETHYLENE GLYCOL (1PEad)
1ae: PENTAETHYLENE GLYCOL (1PEae)
1af: PENTAETHYLENE GLYCOL (1PEaf)
1ag: PENTAETHYLENE GLYCOL (1PEag)
1ah: PENTAETHYLENE GLYCOL (1PEah)
1ai: PENTAETHYLENE GLYCOL (1PEai)
1aj: PENTAETHYLENE GLYCOL (1PEaj)
1ak: PENTAETHYLENE GLYCOL (1PEak)
1al: PENTAETHYLENE GLYCOL (1PEal)
1am: PENTAETHYLENE GLYCOL (1PEam)
1an: PENTAETHYLENE GLYCOL (1PEan)
1ao: PENTAETHYLENE GLYCOL (1PEao)
1ap: PENTAETHYLENE GLYCOL (1PEap)
1aq: PENTAETHYLENE GLYCOL (1PEaq)
1ar: PENTAETHYLENE GLYCOL (1PEar)
1as: PENTAETHYLENE GLYCOL (1PEas)
1at: PENTAETHYLENE GLYCOL (1PEat)
1au: PENTAETHYLENE GLYCOL (1PEau)
1av: PENTAETHYLENE GLYCOL (1PEav)
1aw: PENTAETHYLENE GLYCOL (1PEaw)
1ax: PENTAETHYLENE GLYCOL (1PEax)
1ay: PENTAETHYLENE GLYCOL (1PEay)
1az: PENTAETHYLENE GLYCOL (1PEaz)
1b: PENTAETHYLENE GLYCOL (1PEb)
1ba: PENTAETHYLENE GLYCOL (1PEba)
1bb: PENTAETHYLENE GLYCOL (1PEbb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
1e: PENTAETHYLENE GLYCOL (1PEe)
1f: PENTAETHYLENE GLYCOL (1PEf)
1g: PENTAETHYLENE GLYCOL (1PEg)
1h: PENTAETHYLENE GLYCOL (1PEh)
1i: PENTAETHYLENE GLYCOL (1PEi)
1j: PENTAETHYLENE GLYCOL (1PEj)
1k: PENTAETHYLENE GLYCOL (1PEk)
1l: PENTAETHYLENE GLYCOL (1PEl)
1m: PENTAETHYLENE GLYCOL (1PEm)
1n: PENTAETHYLENE GLYCOL (1PEn)
1o: PENTAETHYLENE GLYCOL (1PEo)
1p: PENTAETHYLENE GLYCOL (1PEp)
1q: PENTAETHYLENE GLYCOL (1PEq)
1r: PENTAETHYLENE GLYCOL (1PEr)
1s: PENTAETHYLENE GLYCOL (1PEs)
1t: PENTAETHYLENE GLYCOL (1PEt)
1u: PENTAETHYLENE GLYCOL (1PEu)
1v: PENTAETHYLENE GLYCOL (1PEv)
1w: PENTAETHYLENE GLYCOL (1PEw)
1x: PENTAETHYLENE GLYCOL (1PEx)
1y: PENTAETHYLENE GLYCOL (1PEy)
1z: PENTAETHYLENE GLYCOL (1PEz)
2a: NONAETHYLENE GLYCOL (2PEa)
2b: NONAETHYLENE GLYCOL (2PEb)
2c: NONAETHYLENE GLYCOL (2PEc)
2d: NONAETHYLENE GLYCOL (2PEd)
3a: CARBONATE ION (CO3a)
3b: CARBONATE ION (CO3b)
3c: CARBONATE ION (CO3c)
3d: CARBONATE ION (CO3d)
3e: CARBONATE ION (CO3e)
3f: CARBONATE ION (CO3f)
3g: CARBONATE ION (CO3g)
3h: CARBONATE ION (CO3h)
3i: CARBONATE ION (CO3i)
3j: CARBONATE ION (CO3j)
3k: CARBONATE ION (CO3k)
3l: CARBONATE ION (CO3l)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
5i: ZINC ION (ZNi)
5j: ZINC ION (ZNj)
5k: ZINC ION (ZNk)
5l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
30
Ligand/Ion
PENTAETHYLENE GLYCOL
2
2PE
1
Ligand/Ion
NONAETHYLENE GLYCOL
3
CO3
6
Ligand/Ion
CARBONATE ION
4
SO4
5
Ligand/Ion
SULFATE ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(52, 52)
Info
All Sites
01: AC4 (SOFTWARE)
02: BC4 (SOFTWARE)
03: BC5 (SOFTWARE)
04: DC3 (SOFTWARE)
05: FC6 (SOFTWARE)
06: FC7 (SOFTWARE)
07: FC8 (SOFTWARE)
08: FC9 (SOFTWARE)
09: GC1 (SOFTWARE)
10: GC2 (SOFTWARE)
11: GC3 (SOFTWARE)
12: GC4 (SOFTWARE)
13: GC5 (SOFTWARE)
14: GC6 (SOFTWARE)
15: GC7 (SOFTWARE)
16: GC8 (SOFTWARE)
17: GC9 (SOFTWARE)
18: HC1 (SOFTWARE)
19: HC2 (SOFTWARE)
20: HC3 (SOFTWARE)
21: HC4 (SOFTWARE)
22: HC5 (SOFTWARE)
23: HC6 (SOFTWARE)
24: HC7 (SOFTWARE)
25: HC8 (SOFTWARE)
26: HC9 (SOFTWARE)
27: IC1 (SOFTWARE)
28: IC2 (SOFTWARE)
29: IC3 (SOFTWARE)
30: IC4 (SOFTWARE)
31: IC5 (SOFTWARE)
32: IC6 (SOFTWARE)
33: IC7 (SOFTWARE)
34: IC8 (SOFTWARE)
35: IC9 (SOFTWARE)
36: JC1 (SOFTWARE)
37: JC2 (SOFTWARE)
38: JC3 (SOFTWARE)
39: JC4 (SOFTWARE)
40: JC5 (SOFTWARE)
41: JC6 (SOFTWARE)
42: JC7 (SOFTWARE)
43: JC8 (SOFTWARE)
44: JC9 (SOFTWARE)
45: KC1 (SOFTWARE)
46: KC2 (SOFTWARE)
47: KC3 (SOFTWARE)
48: KC4 (SOFTWARE)
49: KC5 (SOFTWARE)
50: KC6 (SOFTWARE)
51: KC7 (SOFTWARE)
52: KC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
GLU A:125 , GLY A:126 , LEU A:219 , SER A:220 , HOH A:4029 , LYS G:111
BINDING SITE FOR RESIDUE SO4 A 2
02
BC4
SOFTWARE
2PE B:14 , TYR B:103 , ASN B:104 , 2PE H:6 , TYR H:103 , ASN H:104 , HIS H:108 , GLU H:282 , HOH H:3089 , HOH H:3267
BINDING SITE FOR RESIDUE 2PE B 13
03
BC5
SOFTWARE
2PE B:13 , TYR B:103 , HIS B:108 , LYS B:320 , TYR B:411 , 2PE H:6 , TYR H:103 , GLU H:316 , GLN H:319 , LYS H:320
BINDING SITE FOR RESIDUE 2PE B 14
04
DC3
SOFTWARE
HIS D:108 , ILE D:110 , GLU D:282 , ARG D:285 , HIS L:108 , ILE L:110 , LYS L:111
BINDING SITE FOR RESIDUE 1PE D 612
05
FC6
SOFTWARE
LYS G:374 , ASP G:379 , ASP G:399 , GLU G:461 , HOH G:4256 , HOH G:4257
BINDING SITE FOR RESIDUE ZN G 1001
06
FC7
SOFTWARE
LYS G:374 , ALA G:460 , GLY G:462 , ARG G:463 , LEU G:487 , HOH G:4257
BINDING SITE FOR RESIDUE CO3 G 1002
07
FC8
SOFTWARE
ARG G:586 , HOH G:1824 , HOH G:1897 , HOH G:2767 , ASN I:545 , SER I:549 , HOH I:1784
BINDING SITE FOR RESIDUE SO4 G 23
08
FC9
SOFTWARE
1PE G:58 , TYR G:103 , ASN G:104 , HIS G:108 , TYR G:411
BINDING SITE FOR RESIDUE 1PE G 12
09
GC1
SOFTWARE
MET G:392 , PHE G:398 , THR G:486 , GLY G:489 , LEU G:492 , HOH G:3348 , HOH G:4256
BINDING SITE FOR RESIDUE 1PE G 16
10
GC2
SOFTWARE
TRP G:526 , HOH G:649 , HOH G:656 , HOH G:3290 , TRP L:525
BINDING SITE FOR RESIDUE 1PE G 30
11
GC3
SOFTWARE
TYR A:115 , ASN A:122 , GLU A:124 , TYR A:270 , 1PE G:48 , TYR G:115 , ASN G:122 , GLU G:124 , TYR G:270
BINDING SITE FOR RESIDUE 1PE G 47
12
GC4
SOFTWARE
ASN A:122 , 1PE G:47 , ASN G:122
BINDING SITE FOR RESIDUE 1PE G 48
13
GC5
SOFTWARE
1PE G:12 , TYR G:103 , ASN G:104 , GLU G:316 , GLN G:319 , LYS G:320
BINDING SITE FOR RESIDUE 1PE G 58
14
GC6
SOFTWARE
LYS H:374 , ASP H:379 , ASP H:399 , GLU H:461 , HOH H:4259
BINDING SITE FOR RESIDUE ZN H 1001
15
GC7
SOFTWARE
LYS H:374 , ALA H:460 , GLU H:461 , GLY H:462 , ARG H:463 , LEU H:487
BINDING SITE FOR RESIDUE CO3 H 1002
16
GC8
SOFTWARE
2PE B:13 , 2PE B:14 , TYR B:103 , GLU B:316 , LYS B:320 , HOH B:3232 , TYR H:103 , LYS H:320 , LEU H:321
BINDING SITE FOR RESIDUE 2PE H 6
17
GC9
SOFTWARE
MET H:392 , THR H:486 , GLY H:489 , HOH H:4259 , HOH H:4290
BINDING SITE FOR RESIDUE 1PE H 51
18
HC1
SOFTWARE
GLU G:454 , GLY G:456 , ASP H:394 , LEU H:395 , HOH H:1879 , HOH H:4310
BINDING SITE FOR RESIDUE 1PE H 54
19
HC2
SOFTWARE
LYS I:374 , ASP I:379 , ASP I:399 , GLU I:461 , HOH I:4260 , HOH I:4261
BINDING SITE FOR RESIDUE ZN I 1001
20
HC3
SOFTWARE
LYS I:374 , ALA I:460 , GLU I:461 , GLY I:462 , ARG I:463 , LEU I:487 , HOH I:4261
BINDING SITE FOR RESIDUE CO3 I 1002
21
HC4
SOFTWARE
SER G:435 , LYS G:436 , SER H:435 , LYS H:436 , SER I:435 , LYS I:436
BINDING SITE FOR RESIDUE SO4 I 17
22
HC5
SOFTWARE
1PE I:22 , TYR I:103 , GLU I:316 , LYS I:320
BINDING SITE FOR RESIDUE 1PE I 21
23
HC6
SOFTWARE
1PE I:21 , TYR I:103 , ASN I:104 , HIS I:108 , TYR I:411 , HOH I:962
BINDING SITE FOR RESIDUE 1PE I 22
24
HC7
SOFTWARE
GLY I:390 , MET I:392 , PHE I:398 , GLY I:489 , ALA I:577 , HOH I:4260
BINDING SITE FOR RESIDUE 1PE I 27
25
HC8
SOFTWARE
ILE I:529 , ILE I:530 , ASN I:531 , GLU I:532 , HOH I:1183 , TYR J:499 , HOH J:3537 , HOH J:4349
BINDING SITE FOR RESIDUE 1PE I 61
26
HC9
SOFTWARE
1PE J:15 , LYS J:374 , ASP J:379 , ASP J:399 , GLU J:461 , CO3 J:1002
BINDING SITE FOR RESIDUE ZN J 1001
27
IC1
SOFTWARE
LYS J:374 , ALA J:460 , GLY J:462 , ARG J:463 , LEU J:487 , ZN J:1001
BINDING SITE FOR RESIDUE CO3 J 1002
28
IC2
SOFTWARE
ASN J:545 , SER J:549 , HOH J:663 , HOH J:4241 , HOH J:4278 , ARG K:586 , HOH K:2810
BINDING SITE FOR RESIDUE SO4 J 20
29
IC3
SOFTWARE
TYR J:103 , HIS J:108 , PHE J:289 , LYS J:320 , LEU J:321 , TYR J:411 , HOH J:785
BINDING SITE FOR RESIDUE 1PE J 2
30
IC4
SOFTWARE
GLU J:316 , LYS J:320 , HOH J:3661
BINDING SITE FOR RESIDUE 1PE J 3
31
IC5
SOFTWARE
GLY J:390 , MET J:392 , ASP J:399 , THR J:486 , GLY J:489 , LEU J:492 , ZN J:1001
BINDING SITE FOR RESIDUE 1PE J 15
32
IC6
SOFTWARE
ASN J:449 , LYS J:451 , ARG J:534 , ASP J:543 , GLU J:564 , GLN J:567 , SER K:254
BINDING SITE FOR RESIDUE 1PE J 45
33
IC7
SOFTWARE
HIS F:108 , ASP F:109 , LYS F:111 , ARG F:285 , HIS J:108 , ILE J:110 , LYS J:111 , GLU J:282 , ARG J:285 , HOH J:3642
BINDING SITE FOR RESIDUE 1PE J 49
34
IC8
SOFTWARE
SER J:517 , LYS J:518 , VAL J:524
BINDING SITE FOR RESIDUE 1PE J 60
35
IC9
SOFTWARE
LYS K:374 , ASP K:379 , ASP K:399 , GLU K:461 , HOH K:4264
BINDING SITE FOR RESIDUE ZN K 1001
36
JC1
SOFTWARE
LYS K:374 , ALA K:460 , GLY K:462 , ARG K:463 , LEU K:487
BINDING SITE FOR RESIDUE CO3 K 1002
37
JC2
SOFTWARE
SER J:435 , LYS J:436 , SER K:435 , LYS K:436 , SER L:435 , LYS L:436
BINDING SITE FOR RESIDUE SO4 K 18
38
JC3
SOFTWARE
1PE K:4 , ILE K:101 , GLU K:102 , TYR K:103 , ASN K:104 , HOH K:1969
BINDING SITE FOR RESIDUE SO4 K 19
39
JC4
SOFTWARE
MET K:392 , THR K:486 , LEU K:487 , GLY K:489 , HOH K:4264
BINDING SITE FOR RESIDUE 1PE K 36
40
JC5
SOFTWARE
SO4 K:19 , GLU K:316 , LYS K:320
BINDING SITE FOR RESIDUE 1PE K 4
41
JC6
SOFTWARE
TYR K:103 , HIS K:108 , PHE K:289 , LYS K:320 , TYR K:411 , HOH K:2173
BINDING SITE FOR RESIDUE 1PE K 5
42
JC7
SOFTWARE
ASN K:449 , LYS K:451 , ASP K:543 , GLU K:564 , GLN K:567 , HOH K:2666 , SER L:254
BINDING SITE FOR RESIDUE 1PE K 42
43
JC8
SOFTWARE
LEU K:94 , ASP K:95 , THR K:97
BINDING SITE FOR RESIDUE 1PE K 50
44
JC9
SOFTWARE
SER K:517 , LYS K:518 , VAL K:524 , TRP K:525
BINDING SITE FOR RESIDUE 1PE K 52
45
KC1
SOFTWARE
GLU J:454 , GLY J:456 , HOH J:4241 , ASP K:394 , LEU K:395 , HOH K:2810
BINDING SITE FOR RESIDUE 1PE K 55
46
KC2
SOFTWARE
LYS L:374 , ASP L:379 , ASP L:399 , GLU L:461 , HOH L:4266
BINDING SITE FOR RESIDUE ZN L 1001
47
KC3
SOFTWARE
LYS L:374 , ALA L:460 , GLU L:461 , GLY L:462 , ARG L:463 , LEU L:487 , HOH L:4266
BINDING SITE FOR RESIDUE CO3 L 1002
48
KC4
SOFTWARE
TYR L:103 , ASN L:104 , HIS L:108 , LYS L:320 , TYR L:411 , HOH L:4243
BINDING SITE FOR RESIDUE 1PE L 1
49
KC5
SOFTWARE
SER J:254 , ASN L:449 , LYS L:451 , GLU L:564
BINDING SITE FOR RESIDUE 1PE L 25
50
KC6
SOFTWARE
LEU L:514 , SER L:517 , VAL L:524 , TRP L:525 , HOH L:4242
BINDING SITE FOR RESIDUE 1PE L 29
51
KC7
SOFTWARE
TYR L:103 , GLU L:316 , LYS L:320 , HOH L:3139
BINDING SITE FOR RESIDUE 1PE L 56
52
KC8
SOFTWARE
GLY L:390 , MET L:392 , PHE L:398 , THR L:486 , GLY L:489 , LEU L:492
BINDING SITE FOR RESIDUE 1PE L 59
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Peptidase_M17_3kqxL01 (L:291-598)
1b: PFAM_Peptidase_M17_3kqxL02 (L:291-598)
1c: PFAM_Peptidase_M17_3kqxL03 (L:291-598)
1d: PFAM_Peptidase_M17_3kqxL04 (L:291-598)
1e: PFAM_Peptidase_M17_3kqxL05 (L:291-598)
1f: PFAM_Peptidase_M17_3kqxL06 (L:291-598)
1g: PFAM_Peptidase_M17_3kqxL07 (L:291-598)
1h: PFAM_Peptidase_M17_3kqxL08 (L:291-598)
1i: PFAM_Peptidase_M17_3kqxL09 (L:291-598)
1j: PFAM_Peptidase_M17_3kqxL10 (L:291-598)
1k: PFAM_Peptidase_M17_3kqxL11 (L:291-598)
1l: PFAM_Peptidase_M17_3kqxL12 (L:291-598)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MH
(119)
Family
:
Peptidase_M17
(9)
Plasmodium falciparum (isolate 3D7)
(4)
1a
Peptidase_M17-3kqxL01
L:291-598
1b
Peptidase_M17-3kqxL02
L:291-598
1c
Peptidase_M17-3kqxL03
L:291-598
1d
Peptidase_M17-3kqxL04
L:291-598
1e
Peptidase_M17-3kqxL05
L:291-598
1f
Peptidase_M17-3kqxL06
L:291-598
1g
Peptidase_M17-3kqxL07
L:291-598
1h
Peptidase_M17-3kqxL08
L:291-598
1i
Peptidase_M17-3kqxL09
L:291-598
1j
Peptidase_M17-3kqxL10
L:291-598
1k
Peptidase_M17-3kqxL11
L:291-598
1l
Peptidase_M17-3kqxL12
L:291-598
[
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 G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
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by Chain (Biol. Unit)
by Secondary Structure
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Miscellaneous
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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)
[
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") .
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