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3DWK
Biol. Unit 4
Info
Asym.Unit (363 KB)
Biol.Unit 1 (93 KB)
Biol.Unit 2 (95 KB)
Biol.Unit 3 (95 KB)
Biol.Unit 4 (93 KB)
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(1)
Title
:
IDENTIFICATION OF DYNAMIC STRUCTURAL MOTIFS INVOLVED IN PEPTIDOGLYCAN GLYCOSYLTRANSFER
Authors
:
A. L. Lovering, L. De Castro, N. C. J. Strynadka
Date
:
22 Jul 08 (Deposition) - 30 Sep 08 (Release) - 18 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
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
:
Lysozyme-Fold Transpeptidase Fold Pi-Helix, Cell Shape, Cell Wall Biogenesis/Degradation, Membrane, Peptidoglycan Synthesis, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. L. Lovering, L. De Castro, N. C. Strynadka
Identification Of Dynamic Structural Motifs Involved In Peptidoglycan Glycosyltransfer.
J. Mol. Biol. V. 383 167 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2ak: SULFATE ION (SO4ak)
2al: SULFATE ION (SO4al)
2am: SULFATE ION (SO4am)
2an: SULFATE ION (SO4an)
2ao: SULFATE ION (SO4ao)
2ap: SULFATE ION (SO4ap)
2aq: SULFATE ION (SO4aq)
2ar: SULFATE ION (SO4ar)
2as: SULFATE ION (SO4as)
2at: SULFATE ION (SO4at)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LDA
1
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
2
SO4
9
Ligand/Ion
SULFATE ION
[
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Sites
(12, 12)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC1 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: CC9 (SOFTWARE)
09: DC9 (SOFTWARE)
10: EC1 (SOFTWARE)
11: EC3 (SOFTWARE)
12: EC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
ASN D:602 , GLY D:637 , HIS D:638
BINDING SITE FOR RESIDUE SO4 D 5
02
AC7
SOFTWARE
GLY D:590 , THR D:593 , LYS D:605
BINDING SITE FOR RESIDUE SO4 D 7
03
AC9
SOFTWARE
LYS D:214 , ASN D:220 , ASN D:279 , SER D:670 , ASN D:677 , SER D:679 , GLY D:680 , GLN D:682
BINDING SITE FOR RESIDUE SO4 D 9
04
BC1
SOFTWARE
SER A:639 , GLN A:640 , ARG D:117 , HIS D:121 , ASP D:125 , TYR D:126 , LYS D:127
BINDING SITE FOR RESIDUE SO4 D 10
05
BC2
SOFTWARE
ASN A:602 , GLY A:637 , HIS A:638 , LYS D:127
BINDING SITE FOR RESIDUE SO4 A 11
06
BC3
SOFTWARE
LYS A:628 , SER D:183
BINDING SITE FOR RESIDUE SO4 A 12
07
BC4
SOFTWARE
SER D:398 , SER D:454 , THR D:584 , GLY D:585 , THR D:586
BINDING SITE FOR RESIDUE SO4 D 14
08
CC9
SOFTWARE
THR D:342 , ASN D:345
BINDING SITE FOR RESIDUE SO4 D 30
09
DC9
SOFTWARE
ASP D:241 , HIS D:242 , LYS D:244 , ALA D:245
BINDING SITE FOR RESIDUE SO4 D 39
10
EC1
SOFTWARE
TRP D:415 , SER D:465 , ASN D:469
BINDING SITE FOR RESIDUE SO4 D 40
11
EC3
SOFTWARE
TYR B:173 , TYR B:176 , ARG B:177 , SER D:164 , ILE D:165 , GLY D:166
BINDING SITE FOR RESIDUE SO4 B 42
12
EC8
SOFTWARE
SER A:351 , TYR A:643 , LEU B:129 , GLY B:134 , TYR D:126 , ALA D:169 , ALA D:172 , TYR D:173 , TYR D:176
BINDING SITE FOR RESIDUE LDA D 1
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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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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3dwka1 (A:71-290)
1b: SCOP_d3dwkb1 (B:71-292)
1c: SCOP_d3dwkc1 (C:70-292)
1d: SCOP_d3dwkd1 (D:73-292)
2a: SCOP_d3dwka2 (A:296-692)
2b: SCOP_d3dwkb2 (B:293-692)
2c: SCOP_d3dwkc2 (C:293-692)
2d: SCOP_d3dwkd2 (D:293-692)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lysozyme-like
(1361)
Superfamily
:
Lysozyme-like
(1361)
Family
:
PBP transglycosylase domain-like
(7)
Protein domain
:
Penicillin-binding protein 2, PBP2
(3)
Staphylococcus aureus [TaxId: 1280]
(3)
1a
d3dwka1
A:71-290
1b
d3dwkb1
B:71-292
1c
d3dwkc1
C:70-292
1d
d3dwkd1
D:73-292
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 2, PBP2
(3)
Staphylococcus aureus [TaxId: 1280]
(3)
2a
d3dwka2
A:296-692
2b
d3dwkb2
B:293-692
2c
d3dwkc2
C:293-692
2d
d3dwkd2
D:293-692
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Info
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (363 KB)
Header - Asym.Unit
Biol.Unit 1 (93 KB)
Header - Biol.Unit 1
Biol.Unit 2 (95 KB)
Header - Biol.Unit 2
Biol.Unit 3 (95 KB)
Header - Biol.Unit 3
Biol.Unit 4 (93 KB)
Header - Biol.Unit 4
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