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.
1Z8L
Biol. Unit 2
Info
Asym.Unit (438 KB)
Biol.Unit 1 (216 KB)
Biol.Unit 2 (218 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 PROSTATE-SPECIFIC MEMBRANE ANTIGEN, A TUMOR MARKER AND PEPTIDASE
Authors
:
M. I. Davis, M. J. Bennett, L. M. Thomas, P. J. Bjorkman
Date
:
30 Mar 05 (Deposition) - 19 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Dimeric Protein With Three Domains Of Type A+B, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. I. Davis, M. J. Bennett, L. M. Thomas, P. J. Bjorkman
Crystal Structure Of Prostate-Specific Membrane Antigen, A Tumor Marker And Peptidase
Proc. Natl. Acad. Sci. Usa V. 102 5981 2005
[
close entry info
]
Hetero Components
(2, 24)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
1ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
1ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
1ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
1ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
1af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
1ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
1ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
1ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
1aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
1s: N-ACETYL-D-GLUCOSAMINE (NAGs)
1t: N-ACETYL-D-GLUCOSAMINE (NAGt)
1u: N-ACETYL-D-GLUCOSAMINE (NAGu)
1v: N-ACETYL-D-GLUCOSAMINE (NAGv)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
1y: N-ACETYL-D-GLUCOSAMINE (NAGy)
1z: N-ACETYL-D-GLUCOSAMINE (NAGz)
2a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
2b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
2c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
2d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
2e: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGe)
2f: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGf)
2g: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGg)
2h: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGh)
2i: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGi)
2j: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGj)
2k: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGk)
2l: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGl)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
18
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NDG
6
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(28, 28)
Info
All Sites
01: CC7 (SOFTWARE)
02: CC8 (SOFTWARE)
03: CC9 (SOFTWARE)
04: DC1 (SOFTWARE)
05: DC2 (SOFTWARE)
06: DC3 (SOFTWARE)
07: DC4 (SOFTWARE)
08: DC5 (SOFTWARE)
09: DC6 (SOFTWARE)
10: DC7 (SOFTWARE)
11: DC8 (SOFTWARE)
12: DC9 (SOFTWARE)
13: EC1 (SOFTWARE)
14: EC2 (SOFTWARE)
15: EC3 (SOFTWARE)
16: EC4 (SOFTWARE)
17: EC5 (SOFTWARE)
18: EC6 (SOFTWARE)
19: EC7 (SOFTWARE)
20: EC8 (SOFTWARE)
21: EC9 (SOFTWARE)
22: FC1 (SOFTWARE)
23: FC2 (SOFTWARE)
24: FC3 (SOFTWARE)
25: FC8 (SOFTWARE)
26: FC9 (SOFTWARE)
27: GC1 (SOFTWARE)
28: GC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC7
SOFTWARE
ASN C:76 , GLN C:95 , NDG C:3761
BINDING SITE FOR RESIDUE NAG C 3754
02
CC8
SOFTWARE
GLN C:95 , NAG C:3754
BINDING SITE FOR RESIDUE NDG C 3761
03
CC9
SOFTWARE
ASN C:121 , HIS C:124 , NAG C:3762
BINDING SITE FOR RESIDUE NAG C 3755
04
DC1
SOFTWARE
NAG C:3755
BINDING SITE FOR RESIDUE NAG C 3762
05
DC2
SOFTWARE
ASN C:153 , NDG C:3763
BINDING SITE FOR RESIDUE NDG C 3756
06
DC3
SOFTWARE
NDG C:3756
BINDING SITE FOR RESIDUE NDG C 3763
07
DC4
SOFTWARE
TRP C:246 , ASN C:459 , GLU C:486 , PHE C:565 , TYR C:566 , NAG C:3764
BINDING SITE FOR RESIDUE NAG C 3757
08
DC5
SOFTWARE
NAG C:3757
BINDING SITE FOR RESIDUE NAG C 3764
09
DC6
SOFTWARE
SER C:472 , ASN C:476 , NAG C:3765
BINDING SITE FOR RESIDUE NAG C 3758
10
DC7
SOFTWARE
NAG C:3758
BINDING SITE FOR RESIDUE NAG C 3765
11
DC8
SOFTWARE
SER C:634 , ASN C:638 , GLN C:740 , TYR D:277
BINDING SITE FOR RESIDUE NAG C 3759
12
DC9
SOFTWARE
GLU C:137 , ASN C:140
BINDING SITE FOR RESIDUE NAG C 3760
13
EC1
SOFTWARE
ASN D:76 , GLN D:95 , NDG D:4761
BINDING SITE FOR RESIDUE NAG D 4754
14
EC2
SOFTWARE
GLN D:95 , NAG D:4754
BINDING SITE FOR RESIDUE NDG D 4761
15
EC3
SOFTWARE
ASN D:121 , HIS D:124 , NAG D:4762
BINDING SITE FOR RESIDUE NAG D 4755
16
EC4
SOFTWARE
NAG D:4755
BINDING SITE FOR RESIDUE NAG D 4762
17
EC5
SOFTWARE
ASN D:153 , NDG D:4763
BINDING SITE FOR RESIDUE NDG D 4756
18
EC6
SOFTWARE
NDG D:4756
BINDING SITE FOR RESIDUE NDG D 4763
19
EC7
SOFTWARE
TRP D:246 , ASN D:459 , GLU D:486 , PHE D:565 , TYR D:566 , NAG D:4764
BINDING SITE FOR RESIDUE NAG D 4757
20
EC8
SOFTWARE
NAG D:4757
BINDING SITE FOR RESIDUE NAG D 4764
21
EC9
SOFTWARE
SER D:472 , ASN D:476 , NAG D:4765
BINDING SITE FOR RESIDUE NAG D 4758
22
FC1
SOFTWARE
NAG D:4758
BINDING SITE FOR RESIDUE NAG D 4765
23
FC2
SOFTWARE
TYR C:277 , SER D:634 , ASN D:638 , GLN D:740
BINDING SITE FOR RESIDUE NAG D 4759
24
FC3
SOFTWARE
GLU D:137 , ASN D:140
BINDING SITE FOR RESIDUE NAG D 4760
25
FC8
SOFTWARE
HIS C:377 , ASP C:387 , GLU C:424 , ASP C:453 , ASN C:519 , ZN C:3752 , HOH C:3753
BINDING SITE FOR RESIDUE ZN C 3751
26
FC9
SOFTWARE
ASP C:387 , GLU C:425 , TYR C:552 , HIS C:553 , ZN C:3751 , HOH C:3753
BINDING SITE FOR RESIDUE ZN C 3752
27
GC1
SOFTWARE
HIS D:377 , ASP D:387 , GLU D:424 , ASP D:453 , ASN D:519 , ZN D:4752 , HOH D:4753
BINDING SITE FOR RESIDUE ZN D 4751
28
GC2
SOFTWARE
ASP D:387 , GLU D:425 , TYR D:552 , HIS D:553 , ZN D:4751 , HOH D:4753
BINDING SITE FOR RESIDUE ZN D 4752
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_024592 (Y75H, chain C/D, )
2: VAR_012736 (H475Y, chain C/D, )
3: VAR_028882 (V627L, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024592
Y
75
H
FOLH1_HUMAN
Polymorphism
202676
C/D
Y
75
H
2
UniProt
VAR_012736
H
475
Y
FOLH1_HUMAN
Polymorphism
61886492
C/D
H
475
Y
3
UniProt
VAR_028882
V
627
L
FOLH1_HUMAN
Polymorphism
2988342
C/D
V
627
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1z8la1 (A:594-750)
1b: SCOP_d1z8lb1 (B:594-750)
1c: SCOP_d1z8lc1 (C:594-750)
1d: SCOP_d1z8ld1 (D:594-750)
2a: SCOP_d1z8la3 (A:57-117,A:351-593)
2b: SCOP_d1z8lb3 (B:57-117,B:351-593)
2c: SCOP_d1z8lc3 (C:57-117,C:351-593)
2d: SCOP_d1z8ld3 (D:57-117,D:351-593)
3a: SCOP_d1z8la2 (A:118-350)
3b: SCOP_d1z8lb2 (B:118-350)
3c: SCOP_d1z8lc2 (C:118-350)
3d: SCOP_d1z8ld2 (D:118-350)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
N-cbl like
(37)
Superfamily
:
Transferrin receptor-like dimerisation domain
(18)
Family
:
Transferrin receptor-like dimerisation domain
(18)
Protein domain
:
Glutamate carboxypeptidase II
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d1z8la1
A:594-750
1b
d1z8lb1
B:594-750
1c
d1z8lc1
C:594-750
1d
d1z8ld1
D:594-750
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Zn-dependent exopeptidases
(214)
Family
:
FolH catalytic domain-like
(18)
Protein domain
:
Glutamate carboxypeptidase II FOLH1
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
2a
d1z8la3
A:57-117,A:351-593
2b
d1z8lb3
B:57-117,B:351-593
2c
d1z8lc3
C:57-117,C:351-593
2d
d1z8ld3
D:57-117,D:351-593
Fold
:
The swivelling beta/beta/alpha domain
(136)
Superfamily
:
PA domain
(18)
Family
:
PA domain
(18)
Protein domain
:
Glutamate carboxypeptidase II
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
3a
d1z8la2
A:118-350
3b
d1z8lb2
B:118-350
3c
d1z8lc2
C:118-350
3d
d1z8ld2
D:118-350
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_Peptidase_M28_1z8lD01 (D:370-560)
1b: PFAM_Peptidase_M28_1z8lD02 (D:370-560)
1c: PFAM_Peptidase_M28_1z8lD03 (D:370-560)
1d: PFAM_Peptidase_M28_1z8lD04 (D:370-560)
2a: PFAM_PA_1z8lD05 (D:165-263)
2b: PFAM_PA_1z8lD06 (D:165-263)
2c: PFAM_PA_1z8lD07 (D:165-263)
2d: PFAM_PA_1z8lD08 (D:165-263)
3a: PFAM_TFR_dimer_1z8lD09 (D:626-749)
3b: PFAM_TFR_dimer_1z8lD10 (D:626-749)
3c: PFAM_TFR_dimer_1z8lD11 (D:626-749)
3d: PFAM_TFR_dimer_1z8lD12 (D:626-749)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MH
(119)
Family
:
Peptidase_M28
(38)
Homo sapiens (Human)
(30)
1a
Peptidase_M28-1z8lD01
D:370-560
1b
Peptidase_M28-1z8lD02
D:370-560
1c
Peptidase_M28-1z8lD03
D:370-560
1d
Peptidase_M28-1z8lD04
D:370-560
Clan
:
no clan defined [family: PA]
(15)
Family
:
PA
(15)
Homo sapiens (Human)
(12)
2a
PA-1z8lD05
D:165-263
2b
PA-1z8lD06
D:165-263
2c
PA-1z8lD07
D:165-263
2d
PA-1z8lD08
D:165-263
Clan
:
no clan defined [family: TFR_dimer]
(12)
Family
:
TFR_dimer
(12)
Homo sapiens (Human)
(12)
3a
TFR_dimer-1z8lD09
D:626-749
3b
TFR_dimer-1z8lD10
D:626-749
3c
TFR_dimer-1z8lD11
D:626-749
3d
TFR_dimer-1z8lD12
D:626-749
[
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 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 (438 KB)
Header - Asym.Unit
Biol.Unit 1 (216 KB)
Header - Biol.Unit 1
Biol.Unit 2 (218 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
1Z8L
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help