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2ZC3
Asym. Unit
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Asym.Unit (206 KB)
Biol.Unit 1 (103 KB)
Biol.Unit 2 (102 KB)
Biol.Unit 3 (201 KB)
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(1)
Title
:
PENICILLIN-BINDING PROTEIN 2X (PBP 2X) ACYL-ENZYME COMPLEX (BIAPENEM) FROM STREPTOCOCCUS PNEUMONIAE
Authors
:
M. Yamada, T. Watanabe, Y. Takeuchi
Date
:
02 Nov 07 (Deposition) - 08 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: A,B,C,D,E,F (1x)
Keywords
:
Peptidoglycan Synthesis, Cell Wall, Penicillin-Binding, Antibiotics, Biapenem, Antibiotic Resistance, Cell Cycle, Cell Division, Cell Shape, Cell Wall Biogenesis/Degradation, Membrane, Secreted, Transmembrane, Biosynthetic Protein
(Keyword Search:
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Reference
:
M. Yamada, T. Watanabe, N. Baba, Y. Takeuchi, F. Ohsawa, S. Gomi
Crystal Structures Of Biapenem And Tebipenem Complexed With Penicillin-Binding Proteins 2X And 1A From Streptococcus Pneumoniae
Antimicrob. Agents Chemother. V. 52 2053 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: (4R,5S)-3-(6,7-DIHYDRO-5H-PYRAZOLO... (BMGa)
1b: (4R,5S)-3-(6,7-DIHYDRO-5H-PYRAZOLO... (BMGb)
2a: SULFATE ION (SO4a)
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No.
Name
Count
Type
Full Name
1
BMG
2
Ligand/Ion
(4R,5S)-3-(6,7-DIHYDRO-5H-PYRAZOLO[1,2-A][1,2,4]TRIAZOL-4-IUM-6-YLSULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLATE
2
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(3, 3)
Info
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR E:425 , ARG E:426 , ARG F:654
BINDING SITE FOR RESIDUE SO4 E 901
2
AC2
SOFTWARE
SER B:337 , TRP B:374 , SER B:395 , ASN B:397 , PHE B:450 , THR B:526 , LYS B:547 , SER B:548 , GLY B:549 , THR B:550 , LEU D:203 , LYS D:211
BINDING SITE FOR RESIDUE BMG B 801
3
AC3
SOFTWARE
GLU B:320 , SER E:337 , TRP E:374 , SER E:395 , ASN E:397 , GLN E:452 , LYS E:547 , SER E:548 , GLY E:549 , THR E:550
BINDING SITE FOR RESIDUE BMG E 801
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PASTA (C:632-691,F:632-691|C:692-750,F:69...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PASTA
PS51178
PASTA domain profile.
PBPX_STRPN
632-691
692-750
4
C:632-691
F:632-691
C:692-750
F:692-750
PBPX_STRR6
632-691
692-750
4
C:632-691
F:632-691
C:692-750
F:692-750
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2zc3c1 (C:626-692)
1b: SCOP_d2zc3f1 (F:626-692)
1c: SCOP_d2zc3f2 (F:693-750)
1d: SCOP_d2zc3c2 (C:693-750)
2a: SCOP_d2zc3b_ (B:)
2b: SCOP_d2zc3e_ (E:)
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Protein Domains
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Organisms
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)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Superfamily
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Family
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Protein domain
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(10)
1a
d2zc3c1
C:626-692
1b
d2zc3f1
F:626-692
1c
d2zc3f2
F:693-750
1d
d2zc3c2
C:693-750
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
:
Penicillin-binding protein 2x (pbp-2x), transpeptidase domain
(10)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(10)
2a
d2zc3b_
B:
2b
d2zc3e_
E:
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CATH Domains
(0, 0)
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Transpeptidase_2zc3E01 (E:289-609)
1b: PFAM_Transpeptidase_2zc3E02 (E:289-609)
2a: PFAM_PASTA_2zc3F01 (F:694-750)
2b: PFAM_PASTA_2zc3F02 (F:694-750)
3a: PFAM_PBP_dimer_2zc3D01 (D:73-232)
3b: PFAM_PBP_dimer_2zc3D02 (D:73-232)
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Clan
:
Beta-lactamase
(210)
Family
:
Transpeptidase
(31)
Streptococcus pneumoniae
(9)
1a
Transpeptidase-2zc3E01
E:289-609
1b
Transpeptidase-2zc3E02
E:289-609
Clan
:
no clan defined [family: PASTA]
(12)
Family
:
PASTA
(12)
Streptococcus pneumoniae
(7)
2a
PASTA-2zc3F01
F:694-750
2b
PASTA-2zc3F02
F:694-750
Clan
:
no clan defined [family: PBP_dimer]
(15)
Family
:
PBP_dimer
(15)
Streptococcus pneumoniae
(7)
3a
PBP_dimer-2zc3D01
D:73-232
3b
PBP_dimer-2zc3D02
D:73-232
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Asym.Unit (206 KB)
Header - Asym.Unit
Biol.Unit 1 (103 KB)
Header - Biol.Unit 1
Biol.Unit 2 (102 KB)
Header - Biol.Unit 2
Biol.Unit 3 (201 KB)
Header - Biol.Unit 3
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