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1NE7
Asym. Unit
Info
Asym.Unit (328 KB)
Biol.Unit 1 (320 KB)
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(1)
Title
:
HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE
Authors
:
R. Arreola, B. Valderrama, M. L. Morante, E. Horjales
Date
:
10 Dec 02 (Deposition) - 23 Sep 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
V-Type Like Allosteric Enzyme, Conformational Disorder, Conformational Differences, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Arreola, B. Valderrama, M. L. Morante, E. Horjales
Two Mammalian Glucosamine-6-Phosphate Deaminases: A Structural And Genetic Study.
Febs Lett. V. 551 63 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 31)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE (16Ga)
1b: N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE (16Gb)
1c: N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE (16Gc)
1d: N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE (16Gd)
1e: N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE (16Ge)
1f: N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE (16Gf)
2a: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHA... (AGPa)
2b: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHA... (AGPb)
2c: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHA... (AGPc)
2d: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHA... (AGPd)
2e: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHA... (AGPe)
2f: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHA... (AGPf)
3a: ALPHA-D-GLUCOSE (GLCa)
3b: ALPHA-D-GLUCOSE (GLCb)
3c: ALPHA-D-GLUCOSE (GLCc)
3d: ALPHA-D-GLUCOSE (GLCd)
3e: ALPHA-D-GLUCOSE (GLCe)
3f: ALPHA-D-GLUCOSE (GLCf)
3g: ALPHA-D-GLUCOSE (GLCg)
3h: ALPHA-D-GLUCOSE (GLCh)
3i: ALPHA-D-GLUCOSE (GLCi)
3j: ALPHA-D-GLUCOSE (GLCj)
3k: ALPHA-D-GLUCOSE (GLCk)
3l: ALPHA-D-GLUCOSE (GLCl)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
16G
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2
AGP
6
Ligand/Ion
2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE
3
GLC
12
Ligand/Ion
ALPHA-D-GLUCOSE
4
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:26 , GLC A:295 , HOH A:4317 , HOH A:4328 , HOH A:4401 , HOH A:4574
BINDING SITE FOR RESIDUE GLC A 294
02
AC2
SOFTWARE
PHE A:27 , LYS A:33 , GLC A:294 , HOH A:4328 , HOH A:4349 , HOH A:4356 , HOH A:4557
BINDING SITE FOR RESIDUE GLC A 295
03
AC3
SOFTWARE
MET A:1 , HIS A:262 , HOH A:4325 , SER B:151 , SER B:152 , ARG B:158 , VAL B:159 , LYS B:160 , THR B:161 , HOH B:3299 , HOH B:3379 , HOH B:3410 , HOH B:3436
BINDING SITE FOR RESIDUE 16G B 2299
04
AC4
SOFTWARE
GLN B:26 , GLC B:295 , HOH B:3321 , HOH B:3326 , HOH B:3383 , HOH B:3474 , HOH B:3633
BINDING SITE FOR RESIDUE GLC B 294
05
AC5
SOFTWARE
PHE B:27 , LYS B:33 , GLC B:294 , HOH B:3342 , HOH B:3381 , HOH B:3383 , HOH B:3405
BINDING SITE FOR RESIDUE GLC B 295
06
AC6
SOFTWARE
MET B:1 , HIS B:262 , HOH B:3558 , HOH B:3588 , SER C:151 , SER C:152 , ARG C:158 , VAL C:159 , LYS C:160 , THR C:161 , HOH C:4302 , HOH C:4350 , HOH C:4375 , HOH C:4418 , HOH C:4429 , HOH C:4433 , HOH C:4446 , HOH C:4461
BINDING SITE FOR RESIDUE 16G C 3299
07
AC7
SOFTWARE
GLN C:26 , GLC C:295 , HOH C:4312 , HOH C:4365 , HOH C:4384 , HOH C:4543 , HOH C:4658
BINDING SITE FOR RESIDUE GLC C 294
08
AC8
SOFTWARE
PHE C:27 , LYS C:33 , GLC C:294 , HOH C:4366 , HOH C:4384 , HOH C:4392 , HOH C:4631
BINDING SITE FOR RESIDUE GLC C 295
09
AC9
SOFTWARE
SER A:151 , SER A:152 , ARG A:158 , VAL A:159 , LYS A:160 , THR A:161 , HOH A:4315 , HOH A:4318 , HOH A:4396 , HOH A:4434 , HOH A:4441 , HOH A:4445 , MET C:1 , LYS C:2 , HIS C:262 , HOH C:4612
BINDING SITE FOR RESIDUE 16G A 4299
10
BC1
SOFTWARE
GLN D:26 , GLC D:295 , HOH D:7330 , HOH D:7337 , HOH D:7356 , HOH D:7606
BINDING SITE FOR RESIDUE GLC D 294
11
BC2
SOFTWARE
PHE D:27 , LYS D:33 , GLC D:294 , HOH D:7448 , HOH D:7459 , HOH D:7594
BINDING SITE FOR RESIDUE GLC D 295
12
BC3
SOFTWARE
MET D:1 , HIS D:262 , SER E:151 , SER E:152 , ARG E:158 , VAL E:159 , LYS E:160 , THR E:161 , HOH E:6299 , HOH E:6320 , HOH E:6351 , HOH E:6376 , HOH E:6385 , HOH E:6423 , HOH E:6481
BINDING SITE FOR RESIDUE 16G E 5299
13
BC4
SOFTWARE
GLN E:26 , GLC E:295 , HOH E:6328 , HOH E:6361 , HOH E:6388 , HOH E:6436 , HOH E:6503
BINDING SITE FOR RESIDUE GLC E 294
14
BC5
SOFTWARE
PHE E:27 , LYS E:33 , GLC E:294 , HOH E:6358 , HOH E:6388 , HOH E:6403 , HOH E:6422
BINDING SITE FOR RESIDUE GLC E 295
15
BC6
SOFTWARE
MET E:1 , LYS E:2 , HIS E:262 , HOH E:6312 , HOH E:6472 , HOH E:6568 , SER F:151 , SER F:152 , ARG F:158 , VAL F:159 , LYS F:160 , THR F:161 , HOH F:7312 , HOH F:7343 , HOH F:7373 , HOH F:7426 , HOH F:7463 , HOH F:7510
BINDING SITE FOR RESIDUE 16G F 6299
16
BC7
SOFTWARE
GLN F:26 , GLC F:295 , HOH F:7345 , HOH F:7350 , HOH F:7371 , HOH F:7634
BINDING SITE FOR RESIDUE GLC F 294
17
BC8
SOFTWARE
PHE F:27 , LYS F:33 , GLC F:294 , HOH F:7345 , HOH F:7388 , HOH F:7437 , HOH F:7478 , HOH F:7650
BINDING SITE FOR RESIDUE GLC F 295
18
BC9
SOFTWARE
VAL C:112 , SER D:151 , SER D:152 , ARG D:158 , VAL D:159 , LYS D:160 , THR D:161 , MET D:184 , HOH D:7304 , HOH D:7339 , HOH D:7352 , HOH D:7385 , HOH D:7395 , HOH D:7401 , HOH D:7404 , MET F:1 , LYS F:2 , HIS F:262 , HOH F:7302 , HOH F:7391 , HOH F:7627
BINDING SITE FOR RESIDUE 16G D 7299
19
CC1
SOFTWARE
GLY A:42 , SER A:43 , THR A:44 , ARG A:172 , LYS A:208 , AGP A:2298 , HOH A:4421 , HOH A:4588
BINDING SITE FOR RESIDUE SO4 A 2296
20
CC2
SOFTWARE
GLY B:42 , SER B:43 , THR B:44 , PRO B:45 , LYS B:208 , AGP B:3298 , HOH B:3515 , HOH B:3567 , HOH B:3601
BINDING SITE FOR RESIDUE SO4 B 3296
21
CC3
SOFTWARE
GLY C:42 , SER C:43 , THR C:44 , LYS C:208 , AGP C:4298 , HOH C:4469 , HOH C:4484 , HOH C:4486
BINDING SITE FOR RESIDUE SO4 C 4296
22
CC4
SOFTWARE
LYS A:57 , ARG C:21 , TYR C:55 , ASP C:60 , HOH C:4399 , HOH C:4495 , HOH C:4620
BINDING SITE FOR RESIDUE SO4 C 4297
23
CC5
SOFTWARE
GLY D:42 , SER D:43 , THR D:44 , ARG D:172 , LYS D:208 , AGP D:5298 , HOH D:7457 , HOH D:7583
BINDING SITE FOR RESIDUE SO4 D 5296
24
CC6
SOFTWARE
GLY E:42 , SER E:43 , THR E:44 , LYS E:208 , AGP E:6298 , HOH E:6367 , HOH E:6488 , HOH E:6555
BINDING SITE FOR RESIDUE SO4 E 6296
25
CC7
SOFTWARE
SER F:43 , THR F:44 , LYS F:208 , AGP F:7298 , HOH F:7440 , HOH F:7590 , HOH F:7605 , HOH F:7626 , HOH F:7673
BINDING SITE FOR RESIDUE SO4 F 7296
26
CC8
SOFTWARE
PRO A:40 , THR A:41 , SER A:43 , THR A:44 , MET A:71 , ASP A:72 , GLY A:137 , ILE A:138 , HIS A:143 , ALA A:145 , ARG A:172 , LYS A:208 , SO4 A:2296 , HOH A:4421 , HOH A:4437 , HOH A:4484 , HOH A:4587 , HOH A:4627 , HOH A:4674 , HOH A:4675
BINDING SITE FOR RESIDUE AGP A 2298
27
CC9
SOFTWARE
THR B:41 , GLY B:42 , SER B:43 , THR B:44 , MET B:71 , ASP B:72 , TYR B:85 , GLY B:137 , HIS B:143 , ALA B:145 , PHE B:146 , LYS B:208 , SO4 B:3296 , HOH B:3390 , HOH B:3430 , HOH B:3504 , HOH B:3515 , HOH B:3573 , HOH B:3576 , HOH B:3601
BINDING SITE FOR RESIDUE AGP B 3298
28
DC1
SOFTWARE
GLY C:42 , SER C:43 , THR C:44 , ASP C:72 , TYR C:85 , HIS C:143 , PHE C:146 , ASN C:170 , LYS C:208 , SO4 C:4296 , HOH C:4469 , HOH C:4477 , HOH C:4484 , HOH C:4486 , HOH C:4526
BINDING SITE FOR RESIDUE AGP C 4298
29
DC2
SOFTWARE
THR D:41 , GLY D:42 , SER D:43 , THR D:44 , ASP D:72 , TYR D:85 , GLY D:137 , ILE D:138 , HIS D:143 , ALA D:145 , PHE D:146 , ARG D:172 , LYS D:208 , SO4 D:5296 , HOH D:7332 , HOH D:7425 , HOH D:7428 , HOH D:7457 , HOH D:7462 , HOH D:7583 , HOH D:7586 , HOH D:7662
BINDING SITE FOR RESIDUE AGP D 5298
30
DC3
SOFTWARE
THR E:41 , SER E:43 , THR E:44 , MET E:71 , ASP E:72 , TYR E:85 , GLY E:137 , ILE E:138 , HIS E:143 , ALA E:145 , PHE E:146 , LYS E:208 , SO4 E:6296 , HOH E:6367 , HOH E:6371 , HOH E:6400 , HOH E:6488 , HOH E:6529 , HOH E:6543 , HOH E:6555
BINDING SITE FOR RESIDUE AGP E 6298
31
DC4
SOFTWARE
THR F:41 , THR F:44 , MET F:71 , ASP F:72 , GLY F:137 , ILE F:138 , HIS F:143 , ALA F:145 , LYS F:208 , SO4 F:7296 , HOH F:7322 , HOH F:7389 , HOH F:7440 , HOH F:7441 , HOH F:7590 , HOH F:7598 , HOH F:7605 , HOH F:7626 , HOH F:7673
BINDING SITE FOR RESIDUE AGP F 7298
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: GLC_GALNAC_ISOMERASE (A:125-143,B:125-143,C:125-143,D:12...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLC_GALNAC_ISOMERASE
PS01161
Glucosamine/galactosamine-6-phosphate isomerases signature.
GNPI1_HUMAN
125-143
6
A:125-143
B:125-143
C:125-143
D:125-143
E:125-143
F:125-143
[
close PROSITE info
]
Exons
(6, 36)
Info
All Exons
Exon 1.1m (A:1-42 | B:1-42 | C:1-42 | D:1-42 ...)
Exon 1.2 (A:42-76 | B:42-76 | C:42-76 | D:42...)
Exon 1.3a (A:76-137 | B:76-137 | C:76-137 | D...)
Exon 1.4e (A:137-198 | B:137-198 | C:137-198 ...)
Exon 1.5b (A:199-257 | B:199-257 | C:199-257 ...)
Exon 1.6f (A:257-281 | B:257-274 | C:257-274 ...)
View:
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All Exon Boundaries
1: Boundary 1.1c/1.1m
2: Boundary 1.1m/1.2
3: Boundary 1.2/1.3a
4: Boundary 1.3a/1.4e
5: Boundary 1.4e/1.5b
6: Boundary 1.5b/1.6f
7: Boundary 1.6f/-
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
1.1c
ENST00000311337
1c
ENSE00001912150
chr5:
141392596-141392560
37
GNPI1_HUMAN
-
0
0
-
-
1.1m
ENST00000311337
1m
ENSE00002186228
chr5:
141391606-141391477
130
GNPI1_HUMAN
1-42
42
6
A:1-42
B:1-42
C:1-42
D:1-42
E:1-42
F:1-42
42
42
42
42
42
42
1.2
ENST00000311337
2
ENSE00001798580
chr5:
141387465-141387364
102
GNPI1_HUMAN
42-76
35
6
A:42-76
B:42-76
C:42-76
D:42-76
E:42-76
F:42-76
35
35
35
35
35
35
1.3a
ENST00000311337
3a
ENSE00000814331
chr5:
141385891-141385709
183
GNPI1_HUMAN
76-137
62
6
A:76-137
B:76-137
C:76-137
D:76-137
E:76-137
F:76-137
62
62
62
62
62
62
1.4e
ENST00000311337
4e
ENSE00000814330
chr5:
141384681-141384497
185
GNPI1_HUMAN
137-198
62
6
A:137-198
B:137-198
C:137-198
D:137-198
E:137-198
F:137-198
62
62
62
62
62
62
1.5b
ENST00000311337
5b
ENSE00001736194
chr5:
141382827-141382653
175
GNPI1_HUMAN
199-257
59
6
A:199-257
B:199-257
C:199-257
D:199-257
E:199-257
F:199-257
59
59
59
59
59
59
1.6f
ENST00000311337
6f
ENSE00001859437
chr5:
141381694-141380234
1461
GNPI1_HUMAN
257-289
33
6
A:257-281
B:257-274
C:257-274
D:257-274
E:257-274
F:257-274
25
18
18
18
18
18
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1ne7a_ (A:)
1b: SCOP_d1ne7b_ (B:)
1c: SCOP_d1ne7c_ (C:)
1d: SCOP_d1ne7d_ (D:)
1e: SCOP_d1ne7e_ (E:)
1f: SCOP_d1ne7f_ (F:)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NagB/RpiA/CoA transferase-like
(94)
Superfamily
:
NagB/RpiA/CoA transferase-like
(94)
Family
:
NagB-like
(14)
Protein domain
:
Glucosamine 6-phosphate deaminase/isomerase NagB
(11)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1ne7a_
A:
1b
d1ne7b_
B:
1c
d1ne7c_
C:
1d
d1ne7d_
D:
1e
d1ne7e_
E:
1f
d1ne7f_
F:
[
close SCOP info
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1ne7B00 (B:1-274)
1b: CATH_1ne7C00 (C:1-274)
1c: CATH_1ne7D00 (D:1-274)
1d: CATH_1ne7E00 (E:1-274)
1e: CATH_1ne7F00 (F:1-274)
1f: CATH_1ne7A00 (A:1-281)
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1360, no name defined]
(40)
Human (Homo sapiens)
(1)
1a
1ne7B00
B:1-274
1b
1ne7C00
C:1-274
1c
1ne7D00
D:1-274
1d
1ne7E00
E:1-274
1e
1ne7F00
F:1-274
1f
1ne7A00
A:1-281
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Glucosamine_iso_1ne7F01 (F:11-217)
1b: PFAM_Glucosamine_iso_1ne7F02 (F:11-217)
1c: PFAM_Glucosamine_iso_1ne7F03 (F:11-217)
1d: PFAM_Glucosamine_iso_1ne7F04 (F:11-217)
1e: PFAM_Glucosamine_iso_1ne7F05 (F:11-217)
1f: PFAM_Glucosamine_iso_1ne7F06 (F:11-217)
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Organisms
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Clan
:
ISOCOT_Fold
(53)
Family
:
Glucosamine_iso
(12)
Homo sapiens (Human)
(1)
1a
Glucosamine_iso-1ne7F01
F:11-217
1b
Glucosamine_iso-1ne7F02
F:11-217
1c
Glucosamine_iso-1ne7F03
F:11-217
1d
Glucosamine_iso-1ne7F04
F:11-217
1e
Glucosamine_iso-1ne7F05
F:11-217
1f
Glucosamine_iso-1ne7F06
F:11-217
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Protein
Nucleic
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Chain B
Chain C
Chain D
Chain E
Chain F
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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)
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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") .
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Asym.Unit (328 KB)
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Biol.Unit 1 (320 KB)
Header - Biol.Unit 1
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