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.
1R2Q
Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (73 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 HUMAN RAB5A GTPASE DOMAIN AT 1.05 A RESOLUTION
Authors
:
S. Terzyan, G. Zhu, G. Li, X. C. Zhang
Date
:
29 Sep 03 (Deposition) - 23 Dec 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.05
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Rab, Gtpase, Gnp, Atomic Resolution, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Terzyan, G. Zhu, G. Li, X. C. Zhang
Refinement Of The Structure Of Human Rab5A Gtpase Domain At 1. 05 A Resolution.
Acta Crystallogr. , Sect. D V. 60 54 2004
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-GUANYL... (GNPa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GNP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2
GOL
6
Ligand/Ion
GLYCEROL
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(8, 8)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:34 , THR A:52 , GNP A:200 , HOH A:1400 , HOH A:1401
BINDING SITE FOR RESIDUE MG A 300
2
AC2
SOFTWARE
SER A:29 , ALA A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , SER A:35 , PHE A:45 , HIS A:46 , GLU A:47 , GLN A:49 , SER A:51 , THR A:52 , GLY A:78 , ASN A:133 , LYS A:134 , ASP A:136 , LEU A:137 , SER A:163 , ALA A:164 , LYS A:165 , LYS A:180 , MG A:300 , GOL A:400 , HOH A:1400 , HOH A:1401 , HOH A:1419 , HOH A:1425 , HOH A:1430 , HOH A:1446 , HOH A:1507
BINDING SITE FOR RESIDUE GNP A 200
3
AC3
SOFTWARE
ALA A:30 , GLN A:49 , GNP A:200 , HOH A:1425 , HOH A:1430 , HOH A:1463 , HOH A:1592
BINDING SITE FOR RESIDUE GOL A 400
4
AC4
SOFTWARE
THR A:103 , LYS A:116 , LYS A:140 , GOL A:404 , HOH A:1433 , HOH A:1467
BINDING SITE FOR RESIDUE GOL A 401
5
AC5
SOFTWARE
GLU A:106 , ALA A:109 , ARG A:110 , ASN A:113 , ARG A:141 , ALA A:142 , VAL A:143 , ASP A:144 , HOH A:1445 , HOH A:1451 , HOH A:1604
BINDING SITE FOR RESIDUE GOL A 402
6
AC6
SOFTWARE
ARG A:120 , GLN A:121 , GLU A:172 , HOH A:1415 , HOH A:1512 , HOH A:1569 , HOH A:1578
BINDING SITE FOR RESIDUE GOL A 403
7
AC7
SOFTWARE
ASP A:101 , THR A:103 , LYS A:134 , LEU A:137 , LYS A:140 , GOL A:401
BINDING SITE FOR RESIDUE GOL A 404
8
AC8
SOFTWARE
GLN A:119 , ILE A:126 , ILE A:128 , ASN A:155 , HOH A:1517
BINDING SITE FOR RESIDUE GOL A 405
[
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: RAB (A:15-184)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RAB
PS51419
small GTPase Rab1 family profile.
RAB5A_HUMAN
15-215
1
A:15-184
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.2b (A:15-55)
Exon 1.4c (A:55-105)
Exon 1.5b (A:106-146)
Exon 1.6a (A:147-178)
Exon 1.7e (A:178-184)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2b
2: Boundary 1.2b/1.4c
3: Boundary 1.4c/1.5b
4: Boundary 1.5b/1.6a
5: Boundary 1.6a/1.7e
6: Boundary 1.7e/-
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
1.1a
ENST00000273047
1a
ENSE00001769725
chr3:
19988571-19989013
443
RAB5A_HUMAN
-
0
0
-
-
1.2b
ENST00000273047
2b
ENSE00001162720
chr3:
19992298-19992553
256
RAB5A_HUMAN
1-55
55
1
A:15-55
41
1.4c
ENST00000273047
4c
ENSE00001691424
chr3:
20017093-20017244
152
RAB5A_HUMAN
55-105
51
1
A:55-105
51
1.5b
ENST00000273047
5b
ENSE00001783762
chr3:
20017539-20017661
123
RAB5A_HUMAN
106-146
41
1
A:106-146
41
1.6a
ENST00000273047
6a
ENSE00001688303
chr3:
20019802-20019895
94
RAB5A_HUMAN
147-178
32
1
A:147-178
32
1.7e
ENST00000273047
7e
ENSE00001368096
chr3:
20025200-20026667
1468
RAB5A_HUMAN
178-215
38
1
A:178-184
7
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1r2qa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
G proteins
(693)
Protein domain
:
Rab5a
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d1r2qa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1r2qA00 (A:15-184)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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)
Human (Homo sapiens)
(413)
1a
1r2qA00
A:15-184
[
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 (77 KB)
Header - Asym.Unit
Biol.Unit 1 (73 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
1R2Q
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
