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.
3N2C
Asym. Unit
Info
Asym.Unit (1000 KB)
Biol.Unit 1 (503 KB)
Biol.Unit 2 (501 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 PROLIDASE EAH89906 COMPLEXED WITH N-METHYLPHOSPHONATE-L-PROLINE
Authors
:
Y. Patskovsky, C. Xu, J. M. Sauder, S. K. Burley, F. M. Raushel, S. C. Almo Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
17 May 10 (Deposition) - 02 Jun 10 (Release) - 10 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.81
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: I,J,K,L,M,N,O,P (1x)
Keywords
:
Unknown Source, Amidohydrolase, Sargasso Sea, Structural Genomics, Protein Structure Initiative, Psi, New York Structural Genomix Research Consortium, Prolidase, Nysgxrc, New York Sgx Research Center For Structural Genomics, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. F. Xiang, Y. Patskovsky, C. Xu, A. A. Fedorov, E. V. Fedorov, A. A. Sisco, J. M. Sauder, S. K. Burley, S. C. Almo, F. M. Raushel
Functional Identification And Structure Determination Of Tw Novel Prolidases From Cog1228 In The Amidohydrolase Superfamily .
Biochemistry V. 49 6791 2010
[
close entry info
]
Hetero Components
(3, 64)
Info
All Hetero Components
1a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
1b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
1c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
1d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
1e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
1f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
1g: LYSINE NZ-CARBOXYLIC ACID (KCXg)
1h: LYSINE NZ-CARBOXYLIC ACID (KCXh)
1i: LYSINE NZ-CARBOXYLIC ACID (KCXi)
1j: LYSINE NZ-CARBOXYLIC ACID (KCXj)
1k: LYSINE NZ-CARBOXYLIC ACID (KCXk)
1l: LYSINE NZ-CARBOXYLIC ACID (KCXl)
1m: LYSINE NZ-CARBOXYLIC ACID (KCXm)
1n: LYSINE NZ-CARBOXYLIC ACID (KCXn)
1o: LYSINE NZ-CARBOXYLIC ACID (KCXo)
1p: LYSINE NZ-CARBOXYLIC ACID (KCXp)
2a: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYa)
2b: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYb)
2c: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYc)
2d: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYd)
2e: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYe)
2f: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYf)
2g: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYg)
2h: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYh)
2i: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYi)
2j: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYj)
2k: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYk)
2l: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYl)
2m: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYm)
2n: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYn)
2o: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYo)
2p: 1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-... (LWYp)
3a: ZINC ION (ZNa)
3aa: ZINC ION (ZNaa)
3ab: ZINC ION (ZNab)
3ac: ZINC ION (ZNac)
3ad: ZINC ION (ZNad)
3ae: ZINC ION (ZNae)
3af: ZINC ION (ZNaf)
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)
3i: ZINC ION (ZNi)
3j: ZINC ION (ZNj)
3k: ZINC ION (ZNk)
3l: ZINC ION (ZNl)
3m: ZINC ION (ZNm)
3n: ZINC ION (ZNn)
3o: ZINC ION (ZNo)
3p: ZINC ION (ZNp)
3q: ZINC ION (ZNq)
3r: ZINC ION (ZNr)
3s: ZINC ION (ZNs)
3t: ZINC ION (ZNt)
3u: ZINC ION (ZNu)
3v: ZINC ION (ZNv)
3w: ZINC ION (ZNw)
3x: ZINC ION (ZNx)
3y: ZINC ION (ZNy)
3z: ZINC ION (ZNz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
KCX
16
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
2
LWY
16
Ligand/Ion
1-[(R)-HYDROXY(METHYL)PHOSPHORYL]-L-PROLINE
3
ZN
32
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(48, 48)
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)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:63 , HIS A:65 , KCX A:188 , ASP A:321 , LWY A:427
BINDING SITE FOR RESIDUE ZN A 425
02
AC2
SOFTWARE
KCX A:188 , HIS A:229 , HIS A:249 , LWY A:427
BINDING SITE FOR RESIDUE ZN A 426
03
AC3
SOFTWARE
HIS A:65 , LEU A:73 , HIS A:140 , KCX A:188 , GLY A:194 , VAL A:195 , ALA A:196 , HIS A:229 , TYR A:231 , HIS A:249 , ASP A:321 , ZN A:425 , ZN A:426
BINDING SITE FOR RESIDUE LWY A 427
04
AC4
SOFTWARE
HIS B:63 , HIS B:65 , KCX B:188 , ASP B:321 , LWY B:427
BINDING SITE FOR RESIDUE ZN B 425
05
AC5
SOFTWARE
KCX B:188 , HIS B:229 , HIS B:249 , LWY B:427
BINDING SITE FOR RESIDUE ZN B 426
06
AC6
SOFTWARE
HIS B:63 , HIS B:65 , LEU B:73 , HIS B:140 , KCX B:188 , VAL B:195 , ALA B:196 , HIS B:229 , TYR B:231 , ASP B:321 , ZN B:425 , ZN B:426
BINDING SITE FOR RESIDUE LWY B 427
07
AC7
SOFTWARE
HIS C:63 , HIS C:65 , KCX C:188 , ASP C:321 , LWY C:427
BINDING SITE FOR RESIDUE ZN C 425
08
AC8
SOFTWARE
KCX C:188 , HIS C:229 , HIS C:249 , LWY C:427
BINDING SITE FOR RESIDUE ZN C 426
09
AC9
SOFTWARE
HIS C:63 , HIS C:65 , LEU C:73 , HIS C:140 , KCX C:188 , VAL C:195 , ALA C:196 , HIS C:229 , TYR C:231 , HIS C:249 , ASP C:321 , ZN C:425 , ZN C:426
BINDING SITE FOR RESIDUE LWY C 427
10
BC1
SOFTWARE
HIS D:63 , HIS D:65 , KCX D:188 , ASP D:321 , LWY D:427
BINDING SITE FOR RESIDUE ZN D 425
11
BC2
SOFTWARE
KCX D:188 , HIS D:229 , HIS D:249 , LWY D:427
BINDING SITE FOR RESIDUE ZN D 426
12
BC3
SOFTWARE
HIS D:63 , HIS D:65 , HIS D:140 , KCX D:188 , VAL D:195 , ALA D:196 , HIS D:229 , TYR D:231 , HIS D:249 , TYR D:275 , ASP D:321 , ZN D:425 , ZN D:426
BINDING SITE FOR RESIDUE LWY D 427
13
BC4
SOFTWARE
HIS E:63 , HIS E:65 , KCX E:188 , ASP E:321 , LWY E:427
BINDING SITE FOR RESIDUE ZN E 425
14
BC5
SOFTWARE
KCX E:188 , HIS E:229 , HIS E:249 , LWY E:427
BINDING SITE FOR RESIDUE ZN E 426
15
BC6
SOFTWARE
HIS E:63 , HIS E:65 , HIS E:140 , KCX E:188 , VAL E:195 , ALA E:196 , HIS E:229 , TYR E:231 , HIS E:249 , ASP E:321 , ZN E:425 , ZN E:426
BINDING SITE FOR RESIDUE LWY E 427
16
BC7
SOFTWARE
HIS F:63 , HIS F:65 , ALA F:106 , KCX F:188 , ASP F:321 , LWY F:427
BINDING SITE FOR RESIDUE ZN F 425
17
BC8
SOFTWARE
KCX F:188 , HIS F:229 , HIS F:249 , LWY F:427
BINDING SITE FOR RESIDUE ZN F 426
18
BC9
SOFTWARE
HIS F:63 , HIS F:65 , HIS F:140 , KCX F:188 , GLY F:194 , VAL F:195 , ALA F:196 , HIS F:229 , TYR F:231 , ASP F:321 , ZN F:425 , ZN F:426
BINDING SITE FOR RESIDUE LWY F 427
19
CC1
SOFTWARE
HIS G:63 , HIS G:65 , KCX G:188 , ASP G:321 , LWY G:427
BINDING SITE FOR RESIDUE ZN G 425
20
CC2
SOFTWARE
KCX G:188 , HIS G:229 , HIS G:249 , LWY G:427
BINDING SITE FOR RESIDUE ZN G 426
21
CC3
SOFTWARE
HIS G:63 , HIS G:65 , LEU G:73 , HIS G:140 , KCX G:188 , VAL G:195 , ALA G:196 , HIS G:229 , TYR G:231 , HIS G:249 , ASP G:321 , ZN G:425 , ZN G:426
BINDING SITE FOR RESIDUE LWY G 427
22
CC4
SOFTWARE
HIS H:63 , HIS H:65 , KCX H:188 , ASP H:321 , LWY H:427
BINDING SITE FOR RESIDUE ZN H 425
23
CC5
SOFTWARE
KCX H:188 , HIS H:229 , HIS H:249 , LWY H:427
BINDING SITE FOR RESIDUE ZN H 426
24
CC6
SOFTWARE
HIS H:63 , HIS H:65 , LEU H:73 , HIS H:140 , KCX H:188 , VAL H:195 , ALA H:196 , HIS H:229 , TYR H:231 , ASP H:321 , ZN H:425 , ZN H:426
BINDING SITE FOR RESIDUE LWY H 427
25
CC7
SOFTWARE
HIS I:63 , HIS I:65 , KCX I:188 , ASP I:321 , LWY I:427
BINDING SITE FOR RESIDUE ZN I 425
26
CC8
SOFTWARE
KCX I:188 , HIS I:229 , HIS I:249 , LWY I:427
BINDING SITE FOR RESIDUE ZN I 426
27
CC9
SOFTWARE
HIS I:65 , LEU I:73 , HIS I:140 , KCX I:188 , VAL I:195 , ALA I:196 , TYR I:231 , HIS I:249 , ASP I:321 , ZN I:425 , ZN I:426
BINDING SITE FOR RESIDUE LWY I 427
28
DC1
SOFTWARE
HIS J:63 , HIS J:65 , KCX J:188 , ASP J:321 , LWY J:427
BINDING SITE FOR RESIDUE ZN J 425
29
DC2
SOFTWARE
KCX J:188 , HIS J:229 , HIS J:249 , LWY J:427
BINDING SITE FOR RESIDUE ZN J 426
30
DC3
SOFTWARE
HIS J:63 , HIS J:65 , HIS J:140 , GLY J:194 , VAL J:195 , ALA J:196 , HIS J:229 , TYR J:231 , HIS J:249 , ASP J:321 , ZN J:425 , ZN J:426
BINDING SITE FOR RESIDUE LWY J 427
31
DC4
SOFTWARE
HIS K:63 , HIS K:65 , KCX K:188 , ASP K:321 , LWY K:427
BINDING SITE FOR RESIDUE ZN K 425
32
DC5
SOFTWARE
KCX K:188 , HIS K:229 , HIS K:249 , LWY K:427
BINDING SITE FOR RESIDUE ZN K 426
33
DC6
SOFTWARE
HIS K:63 , HIS K:65 , LEU K:73 , HIS K:140 , KCX K:188 , VAL K:195 , ALA K:196 , HIS K:229 , TYR K:231 , HIS K:249 , ASP K:321 , ZN K:425 , ZN K:426
BINDING SITE FOR RESIDUE LWY K 427
34
DC7
SOFTWARE
HIS L:63 , HIS L:65 , KCX L:188 , ASP L:321 , LWY L:427
BINDING SITE FOR RESIDUE ZN L 425
35
DC8
SOFTWARE
KCX L:188 , HIS L:229 , HIS L:249 , LWY L:427
BINDING SITE FOR RESIDUE ZN L 426
36
DC9
SOFTWARE
HIS L:63 , HIS L:65 , LEU L:73 , HIS L:140 , KCX L:188 , VAL L:195 , ALA L:196 , HIS L:229 , TYR L:231 , HIS L:249 , ASP L:321 , ZN L:425 , ZN L:426
BINDING SITE FOR RESIDUE LWY L 427
37
EC1
SOFTWARE
HIS M:63 , HIS M:65 , KCX M:188 , ASP M:321 , LWY M:427
BINDING SITE FOR RESIDUE ZN M 425
38
EC2
SOFTWARE
KCX M:188 , HIS M:229 , HIS M:249 , LWY M:427
BINDING SITE FOR RESIDUE ZN M 426
39
EC3
SOFTWARE
HIS M:63 , HIS M:65 , LEU M:73 , HIS M:140 , KCX M:188 , VAL M:195 , ALA M:196 , HIS M:229 , TYR M:231 , HIS M:249 , ASP M:321 , ZN M:425 , ZN M:426
BINDING SITE FOR RESIDUE LWY M 427
40
EC4
SOFTWARE
HIS N:63 , HIS N:65 , KCX N:188 , ASP N:321 , ZN N:426 , LWY N:427
BINDING SITE FOR RESIDUE ZN N 425
41
EC5
SOFTWARE
KCX N:188 , HIS N:229 , HIS N:249 , ZN N:425 , LWY N:427
BINDING SITE FOR RESIDUE ZN N 426
42
EC6
SOFTWARE
HIS N:63 , HIS N:65 , HIS N:140 , KCX N:188 , GLY N:194 , VAL N:195 , ALA N:196 , HIS N:229 , TYR N:231 , HIS N:249 , ASP N:321 , ZN N:425 , ZN N:426
BINDING SITE FOR RESIDUE LWY N 427
43
EC7
SOFTWARE
HIS O:63 , HIS O:65 , KCX O:188 , ASP O:321 , LWY O:427
BINDING SITE FOR RESIDUE ZN O 425
44
EC8
SOFTWARE
KCX O:188 , HIS O:229 , HIS O:249 , LWY O:427
BINDING SITE FOR RESIDUE ZN O 426
45
EC9
SOFTWARE
HIS O:63 , HIS O:65 , HIS O:140 , KCX O:188 , VAL O:195 , ALA O:196 , HIS O:229 , TYR O:231 , HIS O:249 , ASP O:321 , ZN O:425 , ZN O:426
BINDING SITE FOR RESIDUE LWY O 427
46
FC1
SOFTWARE
HIS P:63 , HIS P:65 , KCX P:188 , ASP P:321 , LWY P:427
BINDING SITE FOR RESIDUE ZN P 425
47
FC2
SOFTWARE
KCX P:188 , HIS P:229 , HIS P:249 , LWY P:427
BINDING SITE FOR RESIDUE ZN P 426
48
FC3
SOFTWARE
HIS P:63 , HIS P:65 , HIS P:140 , KCX P:188 , GLY P:194 , VAL P:195 , ALA P:196 , HIS P:229 , TYR P:231 , HIS P:249 , ASP P:321 , ZN P:425 , ZN P:426
BINDING SITE FOR RESIDUE LWY P 427
[
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
(0, 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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
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 (1000 KB)
Header - Asym.Unit
Biol.Unit 1 (503 KB)
Header - Biol.Unit 1
Biol.Unit 2 (501 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
3N2C
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help