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1AKL
Asym. Unit
Info
Asym.Unit (85 KB)
Biol.Unit 1 (79 KB)
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(1)
Title
:
ALKALINE PROTEASE FROM PSEUDOMONAS AERUGINOSA IFO3080
Authors
:
H. Miyatake, Y. Hata, T. Fujii, K. Hamada, K. Morihara, Y. Katsube
Date
:
16 Sep 95 (Deposition) - 08 Mar 96 (Release) - 12 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase (Metalloproteinase)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Miyatake, Y. Hata, T. Fujii, K. Hamada, K. Morihara, Y. Katsube
Crystal Structure Of The Unliganded Alkaline Protease From Pseudomonas Aeruginosa Ifo3080 And Its Conformational Changes On Ligand Binding.
J. Biochem. (Tokyo) V. 118 474 1995
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 9)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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: CAT (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:176 , HIS A:180 , HIS A:186 , TYR A:216 , HOH A:1061
BINDING SITE FOR RESIDUE ZN A 500
02
AC2
SOFTWARE
ARG A:253 , GLY A:255 , THR A:257 , ASP A:285 , GLY A:287 , ASP A:290
BINDING SITE FOR RESIDUE CA A 501
03
AC3
SOFTWARE
GLY A:288 , ASP A:290 , THR A:327 , GLU A:329 , HOH A:1028 , HOH A:1252
BINDING SITE FOR RESIDUE CA A 502
04
AC4
SOFTWARE
GLY A:334 , GLY A:336 , ASP A:338 , GLY A:351 , ALA A:353 , ASP A:356
BINDING SITE FOR RESIDUE CA A 503
05
AC5
SOFTWARE
GLY A:352 , ALA A:353 , GLY A:354 , ASP A:356 , GLY A:369 , GLY A:370 , ALA A:371 , ASP A:374
BINDING SITE FOR RESIDUE CA A 504
06
AC6
SOFTWARE
GLY A:370 , GLY A:372 , ASP A:374 , GLN A:399 , ASP A:400 , HOH A:1160
BINDING SITE FOR RESIDUE CA A 505
07
AC7
SOFTWARE
ASN A:343 , VAL A:345 , ASN A:347 , GLY A:360 , LEU A:362 , ASP A:365
BINDING SITE FOR RESIDUE CA A 506
08
AC8
SOFTWARE
GLY A:361 , GLY A:363 , ASP A:365 , GLU A:383 , ASP A:390 , HOH A:1313
BINDING SITE FOR RESIDUE CA A 507
09
AC9
SOFTWARE
ASP A:446 , SER A:448 , ASP A:450 , HIS A:452 , ASP A:454
BINDING SITE FOR RESIDUE CA A 508
10
CAT
AUTHOR
HIS A:176 , HIS A:180 , HIS A:186 , TYR A:216 , HOH A:1061
THE ZINC ION AT THE BOTTOM OF CATALYTIC CLEFT HAS FIVE LIGANDS
[
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]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_APRA_PSEAE_001 (D118H, chain A, )
2: VAR_APRA_PSEAE_002 (G167A, chain A, )
3: VAR_APRA_PSEAE_003 (I341Y, chain A, )
4: VAR_APRA_PSEAE_004 (I445V, chain A, )
5: VAR_APRA_PSEAE_005 (A451R, chain A, )
6: VAR_APRA_PSEAE_006 (V470L, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_APRA_PSEAE_001
*
D
127
H
APRA_PSEAE
---
---
A
D
118
H
2
UniProt
VAR_APRA_PSEAE_002
*
G
176
A
APRA_PSEAE
---
---
A
G
167
A
3
UniProt
VAR_APRA_PSEAE_003
*
I
350
Y
APRA_PSEAE
---
---
A
I
341
Y
4
UniProt
VAR_APRA_PSEAE_004
*
I
454
V
APRA_PSEAE
---
---
A
I
445
V
5
UniProt
VAR_APRA_PSEAE_005
*
A
460
R
APRA_PSEAE
---
---
A
A
451
R
6
UniProt
VAR_APRA_PSEAE_006
*
V
479
L
APRA_PSEAE
---
---
A
V
470
L
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:173-182)
2: HEMOLYSIN_CALCIUM (A:356-374)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
APRA_PSEAE
182-191
1
A:173-182
2
HEMOLYSIN_CALCIUM
PS00330
Hemolysin-type calcium-binding region signature.
APRA_PSEAE
365-383
1
A:356-374
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1akla1 (A:247-470)
2a: SCOP_d1akla2 (A:1-246)
View:
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Classes
(
)
(
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Folds
(
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Single-stranded right-handed beta-helix
(140)
Superfamily
:
beta-Roll
(25)
Family
:
Serralysin-like metalloprotease, C-terminal domain
(24)
Protein domain
:
Metalloprotease
(24)
Pseudomonas aeruginosa [TaxId: 287]
(3)
1a
d1akla1
A:247-470
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
Serralysin-like metalloprotease, catalytic (N-terminal) domain
(25)
Protein domain
:
Metalloprotease
(24)
Pseudomonas aeruginosa [TaxId: 287]
(3)
2a
d1akla2
A:1-246
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1aklA02 (A:18-250)
2a: CATH_1aklA01 (A:1-17,A:251-470)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Collagenase (Catalytic Domain)
(236)
Homologous Superfamily
:
Collagenase (Catalytic Domain)
(234)
Pseudomonas aeruginosa. Organism_taxid: 287. Strain: ifo3080
(1)
1a
1aklA02
A:18-250
Class
:
Mainly Beta
(13760)
Architecture
:
2 Solenoid
(23)
Topology
:
Alkaline Protease, subunit P, domain 1
(23)
Homologous Superfamily
:
Alkaline Protease, subunit P, domain 1
(23)
Pseudomonas aeruginosa. Organism_taxid: 287. Strain: ifo3080
(1)
2a
1aklA01
A:1-17,A:251-470
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
(currently selected atoms:
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)
Protein
Nucleic
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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Miscellaneous
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Example Commands
Example Command
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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)
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