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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1IRI
Asym. Unit
Info
Asym.Unit (371 KB)
Biol.Unit 1 (187 KB)
Biol.Unit 2 (186 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 AUTOCRINE MOTILITY FACTOR COMPLEXED WITH AN INHIBITOR
Authors
:
N. Tanaka, A. Haga, H. Uemura, H. Akiyama, T. Funasaka, H. Nagase, A. Raz, K. T. Nakamura
Date
:
08 Oct 01 (Deposition) - 05 Jun 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Cytokine, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Tanaka, A. Haga, H. Uemura, H. Akiyama, T. Funasaka, H. Nagase, A. Raz, K. T. Nakamura
Inhibition Mechanism Of Cytokine Activity Of Human Autocrine Motility Factor Examined By Crystal Structure Analyses And Site-Directed Mutagenesis Studies.
J. Mol. Biol. V. 318 985 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: ERYTHOSE-4-PHOSPHATE (E4Pa)
1b: ERYTHOSE-4-PHOSPHATE (E4Pb)
1c: ERYTHOSE-4-PHOSPHATE (E4Pc)
1d: ERYTHOSE-4-PHOSPHATE (E4Pd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
E4P
4
Ligand/Ion
ERYTHOSE-4-PHOSPHATE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:157 , GLY A:158 , GLY A:159 , SER A:160 , SER A:210 , LYS A:211 , THR A:212 , THR A:215 , GLN A:354 , GLU A:358 , HOH A:622 , HOH A:654 , HOH A:673 , HOH A:690 , HIS B:389
BINDING SITE FOR RESIDUE E4P A 601
2
AC2
SOFTWARE
HIS A:389 , ILE B:157 , GLY B:159 , SER B:160 , SER B:210 , LYS B:211 , THR B:212 , THR B:215 , GLN B:354 , GLU B:358 , HOH B:609 , HOH B:618 , HOH B:663 , HOH B:686
BINDING SITE FOR RESIDUE E4P B 602
3
AC3
SOFTWARE
ILE C:157 , GLY C:158 , GLY C:159 , SER C:160 , SER C:210 , LYS C:211 , THR C:212 , THR C:215 , GLN C:354 , GLU C:358 , HOH C:623 , HOH C:633 , HOH C:649 , HOH C:668 , HOH C:679 , HIS D:389
BINDING SITE FOR RESIDUE E4P C 603
4
AC4
SOFTWARE
HIS C:389 , ILE D:157 , GLY D:159 , SER D:160 , SER D:210 , LYS D:211 , THR D:212 , THR D:215 , GLN D:354 , GLU D:358 , LYS D:519 , HOH D:629 , HOH D:636
BINDING SITE FOR RESIDUE E4P D 604
[
close Site info
]
SAPs(SNPs)/Variants
(25, 100)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_002516 (T5I, chain A/B/C/D, )
02: VAR_002517 (H20P, chain A/B/C/D, )
03: VAR_002518 (R75G, chain A/B/C/D, )
04: VAR_002519 (R83W, chain A/B/C/D, )
05: VAR_002521 (V101M, chain A/B/C/D, )
06: VAR_002520 (G159S, chain A/B/C/D, )
07: VAR_002522 (T195I, chain A/B/C/D, )
08: VAR_018816 (I208T, chain A/B/C/D, )
09: VAR_002523 (T224M, chain A/B/C/D, )
10: VAR_002524 (R273H, chain A/B/C/D, )
11: VAR_002525 (S278L, chain A/B/C/D, )
12: VAR_002526 (A300P, chain A/B/C/D, )
13: VAR_033943 (R308H, chain A/B/C/D, )
14: VAR_002527 (L339P, chain A/B/C/D, )
15: VAR_002528 (Q343R, chain A/B/C/D, )
16: VAR_002529 (R347C, chain A/B/C/D, )
17: VAR_002530 (R347H, chain A/B/C/D, )
18: VAR_002531 (T375R, chain A/B/C/D, )
19: VAR_002532 (H389R, chain A/B/C/D, )
20: VAR_002533 (R472H, chain A/B/C/D, )
21: VAR_002534 (L487F, chain A/B/C/D, )
22: VAR_002535 (E495K, chain A/B/C/D, )
23: VAR_002536 (L517V, chain A/B/C/D, )
24: VAR_002537 (I525T, chain A/B/C/D, )
25: VAR_002538 (D539N, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_002516
T
5
I
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
T
5
I
02
UniProt
VAR_002517
H
20
P
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
H
20
P
03
UniProt
VAR_002518
R
75
G
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
R
75
G
04
UniProt
VAR_002519
R
83
W
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
R
83
W
05
UniProt
VAR_002521
V
101
M
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
V
101
M
06
UniProt
VAR_002520
G
159
S
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
G
159
S
07
UniProt
VAR_002522
T
195
I
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
T
195
I
08
UniProt
VAR_018816
I
208
T
G6PI_HUMAN
Polymorphism
8191371
A/B/C/D
I
208
T
09
UniProt
VAR_002523
T
224
M
G6PI_HUMAN
Disease (HA-GPID)
61754634
A/B/C/D
T
224
M
10
UniProt
VAR_002524
R
273
H
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
R
273
H
11
UniProt
VAR_002525
S
278
L
G6PI_HUMAN
Disease (HA-GPID)
34306618
A/B/C/D
S
278
L
12
UniProt
VAR_002526
A
300
P
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
A
300
P
13
UniProt
VAR_033943
R
308
H
G6PI_HUMAN
Polymorphism
2230294
A/B/C/D
R
308
H
14
UniProt
VAR_002527
L
339
P
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
L
339
P
15
UniProt
VAR_002528
Q
343
R
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
Q
343
R
16
UniProt
VAR_002529
R
347
C
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
R
347
C
17
UniProt
VAR_002530
R
347
H
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
R
347
H
18
UniProt
VAR_002531
T
375
R
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
T
375
R
19
UniProt
VAR_002532
H
389
R
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
H
389
R
20
UniProt
VAR_002533
R
472
H
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
R
472
H
21
UniProt
VAR_002534
L
487
F
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
L
487
F
22
UniProt
VAR_002535
E
495
K
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
E
495
K
23
UniProt
VAR_002536
L
517
V
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
L
517
V
24
UniProt
VAR_002537
I
525
T
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
I
525
T
25
UniProt
VAR_002538
D
539
N
G6PI_HUMAN
Disease (HA-GPID)
---
A/B/C/D
D
539
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: P_GLUCOSE_ISOMERASE_3 (A:7-553,B:7-553,C:7-553,D:7-553)
2: P_GLUCOSE_ISOMERASE_1 (A:268-281,B:268-281,C:268-281,D:26...)
3: P_GLUCOSE_ISOMERASE_2 (A:502-519,B:502-519,C:502-519,D:50...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
P_GLUCOSE_ISOMERASE_3
PS51463
Glucose-6-phosphate isomerase family profile.
G6PI_HUMAN
7-553
4
A:7-553
B:7-553
C:7-553
D:7-553
2
P_GLUCOSE_ISOMERASE_1
PS00765
Phosphoglucose isomerase signature 1.
G6PI_HUMAN
268-281
4
A:268-281
B:268-281
C:268-281
D:268-281
3
P_GLUCOSE_ISOMERASE_2
PS00174
Phosphoglucose isomerase signature 2.
G6PI_HUMAN
502-519
4
A:502-519
B:502-519
C:502-519
D:502-519
[
close PROSITE info
]
Exons
(18, 72)
Info
All Exons
Exon 1.2a (A:1-41 | B:1-41 | C:1-41 | D:1-41)
Exon 1.2f (A:41-71 | B:41-71 | C:41-71 | D:41...)
Exon 1.3a (A:72-94 | B:72-94 | C:72-94 | D:72...)
Exon 1.3d (A:95-134 | B:95-134 | C:95-134 | D...)
Exon 1.5 (A:135-162 | B:135-162 | C:135-162 ...)
Exon 1.6 (A:163-211 | B:163-211 | C:163-211 ...)
Exon 1.7 (A:212-235 | B:212-235 | C:212-235 ...)
Exon 1.8 (A:236-250 | B:236-250 | C:236-250 ...)
Exon 1.9 (A:251-268 | B:251-268 | C:251-268 ...)
Exon 1.10b (A:269-289 | B:269-289 | C:269-289 ...)
Exon 1.11a (A:289-303 | B:289-303 | C:289-303 ...)
Exon 1.12 (A:304-354 | B:304-354 | C:304-354 ...)
Exon 1.13 (A:355-398 | B:355-398 | C:355-398 ...)
Exon 1.14 (A:398-423 | B:398-423 | C:398-423 ...)
Exon 1.15 (A:424-466 | B:424-466 | C:424-466 ...)
Exon 1.16 (A:467-492 | B:467-492 | C:467-492 ...)
Exon 1.17 (A:492-514 | B:492-514 | C:492-514 ...)
Exon 1.18b (A:514-557 | B:514-557 | C:514-557 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.2a
02: Boundary 1.2a/1.2f
03: Boundary 1.2f/1.3a
04: Boundary 1.3a/1.3d
05: Boundary 1.3d/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10b
11: Boundary 1.10b/1.11a
12: Boundary 1.11a/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/1.15
16: Boundary 1.15/1.16
17: Boundary 1.16/1.17
18: Boundary 1.17/1.18b
19: Boundary 1.18b/-
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
1.2a
ENST00000356487
2a
ENSE00001416274
chr19:
34856069-34856293
225
G6PI_HUMAN
1-41
41
4
A:1-41
B:1-41
C:1-41
D:1-41
41
41
41
41
1.2f
ENST00000356487
2f
ENSE00000696364
chr19:
34857250-34857340
91
G6PI_HUMAN
41-71
31
4
A:41-71
B:41-71
C:41-71
D:41-71
31
31
31
31
1.3a
ENST00000356487
3a
ENSE00000696367
chr19:
34857688-34857756
69
G6PI_HUMAN
72-94
23
4
A:72-94
B:72-94
C:72-94
D:72-94
23
23
23
23
1.3d
ENST00000356487
3d
ENSE00000696369
chr19:
34859488-34859607
120
G6PI_HUMAN
95-134
40
4
A:95-134
B:95-134
C:95-134
D:95-134
40
40
40
40
1.5
ENST00000356487
5
ENSE00000696372
chr19:
34868408-34868491
84
G6PI_HUMAN
135-162
28
4
A:135-162
B:135-162
C:135-162
D:135-162
28
28
28
28
1.6
ENST00000356487
6
ENSE00000696374
chr19:
34868640-34868786
147
G6PI_HUMAN
163-211
49
4
A:163-211
B:163-211
C:163-211
D:163-211
49
49
49
49
1.7
ENST00000356487
7
ENSE00000696376
chr19:
34869839-34869910
72
G6PI_HUMAN
212-235
24
4
A:212-235
B:212-235
C:212-235
D:212-235
24
24
24
24
1.8
ENST00000356487
8
ENSE00000846293
chr19:
34870423-34870467
45
G6PI_HUMAN
236-250
15
4
A:236-250
B:236-250
C:236-250
D:236-250
15
15
15
15
1.9
ENST00000356487
9
ENSE00000846294
chr19:
34872371-34872424
54
G6PI_HUMAN
251-268
18
4
A:251-268
B:251-268
C:251-268
D:251-268
18
18
18
18
1.10b
ENST00000356487
10b
ENSE00001184892
chr19:
34884153-34884213
61
G6PI_HUMAN
269-289
21
4
A:269-289
B:269-289
C:269-289
D:269-289
21
21
21
21
1.11a
ENST00000356487
11a
ENSE00001184887
chr19:
34884633-34884676
44
G6PI_HUMAN
289-303
15
4
A:289-303
B:289-303
C:289-303
D:289-303
15
15
15
15
1.12
ENST00000356487
12
ENSE00001184875
chr19:
34884819-34884971
153
G6PI_HUMAN
304-354
51
4
A:304-354
B:304-354
C:304-354
D:304-354
51
51
51
51
1.13
ENST00000356487
13
ENSE00001184867
chr19:
34887206-34887335
130
G6PI_HUMAN
355-398
44
4
A:355-398
B:355-398
C:355-398
D:355-398
44
44
44
44
1.14
ENST00000356487
14
ENSE00001184862
chr19:
34887486-34887562
77
G6PI_HUMAN
398-423
26
4
A:398-423
B:398-423
C:398-423
D:398-423
26
26
26
26
1.15
ENST00000356487
15
ENSE00001184856
chr19:
34890112-34890240
129
G6PI_HUMAN
424-466
43
4
A:424-466
B:424-466
C:424-466
D:424-466
43
43
43
43
1.16
ENST00000356487
16
ENSE00001184852
chr19:
34890461-34890536
76
G6PI_HUMAN
467-492
26
4
A:467-492
B:467-492
C:467-492
D:467-492
26
26
26
26
1.17
ENST00000356487
17
ENSE00001184847
chr19:
34890624-34890690
67
G6PI_HUMAN
492-514
23
4
A:492-514
B:492-514
C:492-514
D:492-514
23
23
23
23
1.18b
ENST00000356487
18b
ENSE00001423864
chr19:
34890806-34891236
431
G6PI_HUMAN
514-558
45
4
A:514-557
B:514-557
C:514-557
D:514-557
44
44
44
44
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1iria_ (A:)
1b: SCOP_d1irib_ (B:)
1c: SCOP_d1iric_ (C:)
1d: SCOP_d1irid_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
SIS domain
(85)
Superfamily
:
SIS domain
(85)
Family
:
Phosphoglucose isomerase, PGI
(37)
Protein domain
:
Phosphoglucose isomerase, PGI
(24)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1iria_
A:
1b
d1irib_
B:
1c
d1iric_
C:
1d
d1irid_
D:
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1iriA02 (A:100-294)
1b: CATH_1iriB02 (B:100-294)
1c: CATH_1iriC02 (C:100-294)
1d: CATH_1iriD02 (D:100-294)
1e: CATH_1iriA01 (A:2-99,A:295-515)
1f: CATH_1iriB01 (B:2-99,B:295-515)
1g: CATH_1iriC01 (C:2-99,C:295-515)
1h: CATH_1iriD01 (D:2-99,D:295-515)
2a: CATH_1iriA03 (A:516-556)
2b: CATH_1iriB03 (B:516-556)
2c: CATH_1iriC03 (C:516-556)
2d: CATH_1iriD03 (D:516-556)
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
:
Glucose-6-phosphate isomerase like protein; domain 1
(105)
Human (Homo sapiens)
(5)
1a
1iriA02
A:100-294
1b
1iriB02
B:100-294
1c
1iriC02
C:100-294
1d
1iriD02
D:100-294
1e
1iriA01
A:2-99,A:295-515
1f
1iriB01
B:2-99,B:295-515
1g
1iriC01
C:2-99,C:295-515
1h
1iriD01
D:2-99,D:295-515
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Phosphoglucose isomerase, C-terminal domain
(32)
Homologous Superfamily
:
[code=1.10.1390.10, no name defined]
(32)
Human (Homo sapiens)
(5)
2a
1iriA03
A:516-556
2b
1iriB03
B:516-556
2c
1iriC03
C:516-556
2d
1iriD03
D:516-556
[
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
Chain B
Chain C
Chain D
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 (371 KB)
Header - Asym.Unit
Biol.Unit 1 (187 KB)
Header - Biol.Unit 1
Biol.Unit 2 (186 KB)
Header - Biol.Unit 2
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
1IRI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
