PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4B8R
Asym. Unit
Info
Asym.Unit (98 KB)
Biol.Unit 1 (91 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)
Authors
:
A. Herrera-Morande, J. A. Rivas-Pardo, F. J. Fernandez, V. Guixe, M. C.
Date
:
30 Aug 12 (Deposition) - 10 Jul 13 (Release) - 17 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Transferase, Ribokinase Superfamily
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. A. Rivas-Pardo, A. Herrera-Morande, V. Castro-Fernandez, F. J. Fernandez, M. C. Vega, V. Guixe
Crystal Structure, Saxs And Kinetic Mechanism Of Hyperthermophilic Adp-Dependent Glucokinase From Thermococcus Litoralis Reveal A Conserved Mechanism For Catalysis.
Plos One V. 8 66687 2013
[
close entry info
]
Hetero Components
(6, 33)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
1b: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
3b: DI(HYDROXYETHYL)ETHER (PEGb)
3c: DI(HYDROXYETHYL)ETHER (PEGc)
3d: DI(HYDROXYETHYL)ETHER (PEGd)
3e: DI(HYDROXYETHYL)ETHER (PEGe)
4a: TRIETHYLENE GLYCOL (PGEa)
4b: TRIETHYLENE GLYCOL (PGEb)
4c: TRIETHYLENE GLYCOL (PGEc)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
6a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
6b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTT
2
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
2
GOL
15
Ligand/Ion
GLYCEROL
3
PEG
5
Ligand/Ion
DI(HYDROXYETHYL)ETHER
4
PGE
3
Ligand/Ion
TRIETHYLENE GLYCOL
5
SO4
6
Ligand/Ion
SULFATE ION
6
TRS
2
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(33, 33)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:233
BINDING SITE FOR RESIDUE GOL A1468
02
AC2
SOFTWARE
LYS A:45 , TYR A:46 , ASP A:51 , TRP A:111 , ASP A:114 , HOH A:2044 , HOH A:2046 , HOH A:2081
BINDING SITE FOR RESIDUE GOL A1469
03
AC3
SOFTWARE
ALA A:281 , TYR A:282 , ASN A:305 , VAL A:307 , GLU A:308
BINDING SITE FOR RESIDUE GOL A1470
04
AC4
SOFTWARE
MET A:341 , ASP A:342 , GLN A:362 , ASP A:429 , ARG A:430 , GOL A:1475
BINDING SITE FOR RESIDUE GOL A1471
05
AC5
SOFTWARE
TYR A:354 , ASN A:403 , ARG A:405 , PGE A:1494 , SO4 A:1498 , HOH A:2227
BINDING SITE FOR RESIDUE GOL A1472
06
AC6
SOFTWARE
ALA A:379 , ALA A:380 , LYS A:438 , ILE A:439 , VAL A:440 , ILE A:449 , HOH A:2228 , HOH A:2272 , HOH A:2282
BINDING SITE FOR RESIDUE GOL A1473
07
AC7
SOFTWARE
GLU A:102 , ARG A:106 , ARG A:109 , PHE A:420 , GLU A:421 , HOH A:2068 , HOH A:2078
BINDING SITE FOR RESIDUE GOL A1474
08
AC8
SOFTWARE
ASP A:342 , GLU A:343 , GOL A:1471
BINDING SITE FOR RESIDUE GOL A1475
09
AC9
SOFTWARE
VAL A:159 , PRO A:160 , ALA A:175 , ARG A:220 , GLU A:222 , SO4 A:1500 , HOH A:2101 , HOH A:2283
BINDING SITE FOR RESIDUE GOL A1476
10
BC1
SOFTWARE
PRO A:71 , ARG A:87 , LYS A:93 , MET A:95 , TRP A:97 , HOH A:2053 , HOH A:2065
BINDING SITE FOR RESIDUE GOL A1477
11
BC2
SOFTWARE
ASP A:260 , ARG A:261 , SER A:264 , GLU A:327 , HIS A:329 , HOH A:2183 , HOH A:2189
BINDING SITE FOR RESIDUE GOL A1478
12
BC3
SOFTWARE
PHE A:162 , GLY A:164 , ASP A:174 , ILE A:176 , ARG A:221 , HOH A:2123 , HOH A:2133
BINDING SITE FOR RESIDUE GOL A1479
13
BC4
SOFTWARE
SER A:101 , GLU A:102 , GLU A:103
BINDING SITE FOR RESIDUE GOL A1480
14
BC5
SOFTWARE
THR A:446 , VAL A:447 , GLY A:448 , ILE A:449 , GLY A:450 , HOH A:2274 , HOH A:2285
BINDING SITE FOR RESIDUE GOL A1481
15
BC6
SOFTWARE
SER A:264 , ASN A:267 , ARG A:271 , HOH A:2189 , HOH A:2193
BINDING SITE FOR RESIDUE GOL A1482
16
BC7
SOFTWARE
TYR A:282 , ARG A:286 , ARG A:289 , SER A:311 , GLU A:314 , PEG A:1487
BINDING SITE FOR RESIDUE TRS A1483
17
BC8
SOFTWARE
GLU A:279 , GLY A:303 , LEU A:304 , ASN A:305 , GLU A:308 , HIS A:352 , GLY A:450 , ASP A:451
BINDING SITE FOR RESIDUE TRS A1484
18
BC9
SOFTWARE
ASN A:40 , ASP A:42 , GLU A:96 , GLY A:119 , GLY A:120 , ILE A:124 , HIS A:184 , ILE A:207
BINDING SITE FOR RESIDUE DTT A1485
19
CC1
SOFTWARE
ARG A:369 , GLU A:421 , ASN A:422 , HOH A:2018 , HOH A:2287
BINDING SITE FOR RESIDUE DTT A1486
20
CC2
SOFTWARE
ALA A:310 , GLU A:314 , TRS A:1483
BINDING SITE FOR RESIDUE PEG A1487
21
CC3
SOFTWARE
LYS A:2 , ARG A:8 , PRO A:142 , TYR A:213 , TYR A:218 , MET A:219 , ARG A:220 , VAL A:408 , GLU A:411 , HOH A:2105
BINDING SITE FOR RESIDUE PEG A1488
22
CC4
SOFTWARE
ARG A:117 , ILE A:118 , ASN A:127 , GLU A:150 , LEU A:151 , PHE A:152
BINDING SITE FOR RESIDUE PEG A1489
23
CC5
SOFTWARE
GLU A:247 , TYR A:248 , ASN A:285
BINDING SITE FOR RESIDUE PEG A1490
24
CC6
SOFTWARE
ARG A:271 , TYR A:272
BINDING SITE FOR RESIDUE PEG A1491
25
CC7
SOFTWARE
GLU A:347 , TYR A:363 , GLU A:461 , ARG A:465 , SO4 A:1495 , HOH A:2196 , HOH A:2288
BINDING SITE FOR RESIDUE PGE A1492
26
CC8
SOFTWARE
ASN A:270 , ASN A:273 , VAL A:274 , LYS A:275 , PRO A:297 , THR A:300 , GLU A:347 , HOH A:2207
BINDING SITE FOR RESIDUE PGE A1493
27
CC9
SOFTWARE
ARG A:224 , ARG A:261 , GLY A:328 , HIS A:329 , ILE A:330 , GLU A:412 , GOL A:1472 , HOH A:2217
BINDING SITE FOR RESIDUE PGE A1494
28
DC1
SOFTWARE
ASN A:273 , LYS A:275 , PGE A:1492 , HOH A:2195
BINDING SITE FOR RESIDUE SO4 A1495
29
DC2
SOFTWARE
LYS A:385 , ARG A:390 , GLN A:393
BINDING SITE FOR RESIDUE SO4 A1496
30
DC3
SOFTWARE
ARG A:117 , GLU A:188 , ARG A:205 , LYS A:444 , SER A:445 , THR A:446 , VAL A:447
BINDING SITE FOR RESIDUE SO4 A1497
31
DC4
SOFTWARE
ARG A:224 , ARG A:405 , GOL A:1472 , HOH A:2256 , HOH A:2257 , HOH A:2290 , HOH A:2291
BINDING SITE FOR RESIDUE SO4 A1498
32
DC5
SOFTWARE
ARG A:134
BINDING SITE FOR RESIDUE SO4 A1499
33
DC6
SOFTWARE
ARG A:220 , ARG A:221 , GLU A:222 , LYS A:415 , GOL A:1476 , HOH A:2122 , HOH A:2156 , HOH A:2283 , HOH A:2284
BINDING SITE FOR RESIDUE SO4 A1500
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: ADPK (A:10-467)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADPK
PS51255
ADP-dependent kinase (ADPK) domain profile.
GLKA_THELN
10-467
1
A:10-467
[
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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4b8ra_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribokinase-like
(226)
Superfamily
:
Ribokinase-like
(189)
Family
:
automated matches
(88)
Protein domain
:
automated matches
(88)
Thermococcus litoralis [TaxId: 2265]
(2)
1a
d4b8ra_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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...
[
close
]
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
]
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:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (98 KB)
Header - Asym.Unit
Biol.Unit 1 (91 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4B8R
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help