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1XP4
Biol. Unit 1
Info
Asym.Unit (236 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (58 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (57 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A PEPTIDOGLYCAN SYNTHESIS REGULATORY FACTOR (PBP3) FROM STREPTOCOCCUS PNEUMONIAE
Authors
:
C. Morlot, L. Pernot, A. Le Gouellec, A. M. Di Guilmi, T. Vernet, O. Dideberg, A. Dessen
Date
:
08 Oct 04 (Deposition) - 09 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Five-Stranded Antiparallel Beta-Sheet, Omega-Like Loop, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Morlot, L. Pernot, A. Le Gouellec, A. M. Di Guilmi, T. Vernet, O. Dideberg, A. Dessen
Crystal Structure Of A Peptidoglycan Synthesis Regulatory Factor (Pbp3) From Streptococcus Pneumoniae
J. Biol. Chem. V. 280 15984 2005
(for further references see the
PDB file header
)
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: IODIDE ION (IODa)
1b: IODIDE ION (IODb)
1c: IODIDE ION (IODc)
1d: IODIDE ION (IODd)
1e: IODIDE ION (IODe)
1f: IODIDE ION (IODf)
1g: IODIDE ION (IODg)
1h: IODIDE ION (IODh)
1i: IODIDE ION (IODi)
1j: IODIDE ION (IODj)
1k: IODIDE ION (IODk)
1l: IODIDE ION (IODl)
1m: IODIDE ION (IODm)
1n: IODIDE ION (IODn)
1o: IODIDE ION (IODo)
1p: IODIDE ION (IODp)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IOD
4
Ligand/Ion
IODIDE ION
2
MSE
9
Mod. Amino Acid
SELENOMETHIONINE
3
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:56 , SER A:119 , LYS A:239 , THR A:240 , THR A:242 , HOH A:597
BINDING SITE FOR RESIDUE SO4 A 464
2
AC5
SOFTWARE
GLN A:374
BINDING SITE FOR RESIDUE IOD A 468
3
AC6
SOFTWARE
PRO A:275
BINDING SITE FOR RESIDUE IOD A 470
4
AC7
SOFTWARE
GLN A:201
BINDING SITE FOR RESIDUE IOD A 471
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1xp4a1 (A:294-386)
1b: SCOP_d1xp4b1 (B:294-386)
1c: SCOP_d1xp4c1 (C:294-386)
1d: SCOP_d1xp4d1 (D:294-386)
2a: SCOP_d1xp4a2 (A:25-293)
2b: SCOP_d1xp4b2 (B:25-293)
2c: SCOP_d1xp4c2 (C:25-293)
2d: SCOP_d1xp4d2 (D:25-293)
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Classes
(
)
(
)
Folds
(
)
(
)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Penicillin-binding protein associated domain
(19)
Superfamily
:
Penicillin-binding protein associated domain
(19)
Family
:
PBP5 C-terminal domain-like
(12)
Protein domain
:
D,D-carboxypeptidase DacA, C-terminal domain
(1)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(1)
1a
d1xp4a1
A:294-386
1b
d1xp4b1
B:294-386
1c
d1xp4c1
C:294-386
1d
d1xp4d1
D:294-386
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta-lactamase/transpeptidase-like
(515)
Superfamily
:
beta-lactamase/transpeptidase-like
(515)
Family
:
beta-Lactamase/D-ala carboxypeptidase
(411)
Protein domain
:
D,D-carboxypeptidase DacA, N-terminal domain
(1)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(1)
2a
d1xp4a2
A:25-293
2b
d1xp4b2
B:25-293
2c
d1xp4c2
C:25-293
2d
d1xp4d2
D:25-293
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1xp4A01 (A:25-293)
1b: CATH_1xp4C01 (C:25-293)
1c: CATH_1xp4B01 (B:25-293)
1d: CATH_1xp4D01 (D:25-293)
2a: CATH_1xp4C02 (C:294-392)
2b: CATH_1xp4A02 (A:294-393)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
Streptococcus pneumoniae r6. Organism_taxid: 171101. Strain: atcc baa-255 / r6.
(1)
1a
1xp4A01
A:25-293
1b
1xp4C01
C:25-293
1c
1xp4B01
B:25-293
1d
1xp4D01
D:25-293
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
(13)
Homologous Superfamily
:
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
(13)
Streptococcus pneumoniae r6. Organism_taxid: 171101. Strain: atcc baa-255 / r6.
(1)
2a
1xp4C02
C:294-392
2b
1xp4A02
A:294-393
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_S11_1xp4D01 (D:25-270)
1b: PFAM_Peptidase_S11_1xp4D02 (D:25-270)
1c: PFAM_Peptidase_S11_1xp4D03 (D:25-270)
1d: PFAM_Peptidase_S11_1xp4D04 (D:25-270)
2a: PFAM_PBP5_C_1xp4D05 (D:293-386)
2b: PFAM_PBP5_C_1xp4D06 (D:293-386)
2c: PFAM_PBP5_C_1xp4D07 (D:293-386)
2d: PFAM_PBP5_C_1xp4D08 (D:293-386)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta-lactamase
(210)
Family
:
Peptidase_S11
(12)
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
(1)
1a
Peptidase_S11-1xp4D01
D:25-270
1b
Peptidase_S11-1xp4D02
D:25-270
1c
Peptidase_S11-1xp4D03
D:25-270
1d
Peptidase_S11-1xp4D04
D:25-270
Clan
:
no clan defined [family: PBP5_C]
(10)
Family
:
PBP5_C
(10)
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
(1)
2a
PBP5_C-1xp4D05
D:293-386
2b
PBP5_C-1xp4D06
D:293-386
2c
PBP5_C-1xp4D07
D:293-386
2d
PBP5_C-1xp4D08
D:293-386
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