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1VIX
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (131 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A PUTATIVE PEPTIDASE T
Authors
:
Structural Genomix
Date
:
01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Structural Genomics, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 16)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
1l: SULFATE ION (SO4l)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
12
Ligand/Ion
SULFATE ION
2
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:78 , ASP A:140 , GLU A:173 , GLU A:174 , ASP A:196 , ZN A:420
BINDING SITE FOR RESIDUE ZN A 419
02
AC2
SOFTWARE
ASP A:140 , GLU A:174 , HIS A:379 , ZN A:419
BINDING SITE FOR RESIDUE ZN A 420
03
AC3
SOFTWARE
HIS B:78 , ASP B:140 , GLU B:173 , ASP B:196 , ZN B:420
BINDING SITE FOR RESIDUE ZN B 419
04
AC4
SOFTWARE
ASP B:140 , GLU B:174 , HIS B:379 , ZN B:419
BINDING SITE FOR RESIDUE ZN B 420
05
AC5
SOFTWARE
HIS A:306 , PRO A:307 , PRO A:330 , HIS A:331 , ARG A:407
BINDING SITE FOR RESIDUE SO4 A 421
06
AC6
SOFTWARE
GLY A:380 , LYS A:381 , HIS A:382
BINDING SITE FOR RESIDUE SO4 A 422
07
AC7
SOFTWARE
LYS A:216 , ARG A:272
BINDING SITE FOR RESIDUE SO4 A 423
08
AC8
SOFTWARE
LYS A:88 , SO4 A:424 , HOH A:435 , LYS B:88 , SO4 B:425
BINDING SITE FOR RESIDUE SO4 B 421
09
AC9
SOFTWARE
LYS B:216 , ARG B:272
BINDING SITE FOR RESIDUE SO4 B 422
10
BC1
SOFTWARE
LYS A:88 , SO4 A:425 , LYS B:88 , SO4 B:421
BINDING SITE FOR RESIDUE SO4 A 424
11
BC2
SOFTWARE
HIS A:223 , ARG B:280 , TYR B:319 , GLY B:354
BINDING SITE FOR RESIDUE SO4 B 423
12
BC3
SOFTWARE
PRO B:330 , HIS B:331 , ARG B:407
BINDING SITE FOR RESIDUE SO4 B 424
13
BC4
SOFTWARE
ASP A:15 , GLN A:17 , LYS A:88 , HOH A:471 , SO4 B:421
BINDING SITE FOR RESIDUE SO4 B 425
14
BC5
SOFTWARE
SO4 A:424 , ASP B:15 , HOH B:433
BINDING SITE FOR RESIDUE SO4 A 425
15
BC6
SOFTWARE
GLU A:29 , TRP A:32 , HIS A:36
BINDING SITE FOR RESIDUE SO4 A 426
16
BC7
SOFTWARE
TRP B:32 , HIS B:36
BINDING SITE FOR RESIDUE SO4 B 426
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ARGE_DAPE_CPG2_1 (A:73-82,B:73-82)
2: ARGE_DAPE_CPG2_2 (A:138-176,B:138-176)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ARGE_DAPE_CPG2_1
PS00758
ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.
PEPT_ECOLI
73-82
2
A:73-82
B:73-82
2
ARGE_DAPE_CPG2_2
PS00759
ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.
PEPT_ECOLI
138-176
2
A:138-176
B:138-176
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1vixa2 (A:208-320)
1b: SCOP_d1vixb2 (B:208-320)
2a: SCOP_d1vixa1 (A:-1-207,A:321-409)
2b: SCOP_d1vixb1 (B:-1-207,B:321-408)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Bacterial exopeptidase dimerisation domain
(12)
Family
:
Bacterial exopeptidase dimerisation domain
(12)
Protein domain
:
Peptidase T (tripeptidase)
(2)
Escherichia coli [TaxId: 562]
(1)
1a
d1vixa2
A:208-320
1b
d1vixb2
B:208-320
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Zn-dependent exopeptidases
(214)
Family
:
Bacterial dinuclear zinc exopeptidases
(55)
Protein domain
:
Peptidase T (tripeptidase), catalytic domain
(2)
Escherichia coli [TaxId: 562]
(1)
2a
d1vixa1
A:-1-207,A:321-409
2b
d1vixb1
B:-1-207,B:321-408
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1vixA02 (A:208-319)
1b: CATH_1vixB02 (B:208-319)
2a: CATH_1vixB01 (B:-1-207,B:320-408)
2b: CATH_1vixA01 (A:-1-207,A:320-409)
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)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.360, no name defined]
(23)
Escherichia coli. Organism_taxid: 562.
(1)
1a
1vixA02
A:208-319
1b
1vixB02
B:208-319
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aminopeptidase
(284)
Homologous Superfamily
:
Zn peptidases
(137)
Escherichia coli. Organism_taxid: 562.
(1)
2a
1vixB01
B:-1-207,B:320-408
2b
1vixA01
A:-1-207,A:320-409
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M20_1vixB01 (B:74-403)
1b: PFAM_Peptidase_M20_1vixB02 (B:74-403)
2a: PFAM_M20_dimer_1vixB03 (B:205-308)
2b: PFAM_M20_dimer_1vixB04 (B:205-308)
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Clans
(
)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MH
(119)
Family
:
Peptidase_M20
(17)
Escherichia coli (strain K12)
(2)
1a
Peptidase_M20-1vixB01
B:74-403
1b
Peptidase_M20-1vixB02
B:74-403
Clan
:
no clan defined [family: M20_dimer]
(13)
Family
:
M20_dimer
(13)
Escherichia coli (strain K12)
(1)
2a
M20_dimer-1vixB03
B:205-308
2b
M20_dimer-1vixB04
B:205-308
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Asymmetric Unit 1
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