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1XP4
Asym. Unit
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, 56)
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
16
Ligand/Ion
IODIDE ION
2
MSE
36
Mod. Amino Acid
SELENOMETHIONINE
3
SO4
4
Ligand/Ion
SULFATE ION
[
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]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
AC2
SOFTWARE
SER B:56 , SER B:119 , THR B:240 , THR B:242 , HOH B:495
BINDING SITE FOR RESIDUE SO4 B 465
03
AC3
SOFTWARE
SER C:56 , SER C:97 , SER C:119 , THR C:221 , THR C:240 , GLY C:241 , THR C:242
BINDING SITE FOR RESIDUE SO4 C 466
04
AC4
SOFTWARE
SER D:56 , SER D:119 , LYS D:239 , THR D:240 , THR D:242 , HOH D:585
BINDING SITE FOR RESIDUE SO4 D 467
05
AC5
SOFTWARE
GLN A:374
BINDING SITE FOR RESIDUE IOD A 468
06
AC6
SOFTWARE
PRO A:275
BINDING SITE FOR RESIDUE IOD A 470
07
AC7
SOFTWARE
GLN A:201
BINDING SITE FOR RESIDUE IOD A 471
08
AC8
SOFTWARE
GLU B:45 , GLN B:374
BINDING SITE FOR RESIDUE IOD B 472
09
AC9
SOFTWARE
PHE B:279
BINDING SITE FOR RESIDUE IOD B 474
10
BC1
SOFTWARE
GLN C:374
BINDING SITE FOR RESIDUE IOD C 476
11
BC2
SOFTWARE
TYR C:223 , PRO C:275
BINDING SITE FOR RESIDUE IOD C 478
12
BC3
SOFTWARE
GLU D:45 , GLN D:374
BINDING SITE FOR RESIDUE IOD D 481
13
BC4
SOFTWARE
TYR D:276
BINDING SITE FOR RESIDUE IOD D 482
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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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, 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)
View:
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
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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
[
close SCOP info
]
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)
View:
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Classes
(
)
(
)
Architectures
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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
[
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]
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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Asym.Unit (236 KB)
Header - Asym.Unit
Biol.Unit 1 (63 KB)
Header - Biol.Unit 1
Biol.Unit 2 (58 KB)
Header - Biol.Unit 2
Biol.Unit 3 (62 KB)
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Biol.Unit 4 (57 KB)
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