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3BAA
Asym. Unit
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Asym.Unit (64 KB)
Biol.Unit 1 (60 KB)
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(1)
Title
:
STRUCTURAL BASIS FOR THE INHIBITION OF BACTERIAL NAD+ DEPENDENT DNA LIGASE
Authors
:
C. Pinko
Date
:
07 Nov 07 (Deposition) - 11 Nov 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Adenylation Domain, Dna Damage, Dna Repair, Dna Replication, Ligase, Nad
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Pinko, A. Borchardt, V. Nikulin, Y. Su
Structural Basis For The Inhibition Of Bacterial Nad+ Dependent Dna Ligase
To Be Published
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: 7-AMINO-2-TERT-BUTYL-4-{[2-(1H-IMI... (3BAa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: BETA-NICOTINAMIDE RIBOSE MONOPHOSP... (NMNa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
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Label:
No.
Name
Count
Type
Full Name
1
3BA
1
Ligand/Ion
7-AMINO-2-TERT-BUTYL-4-{[2-(1H-IMIDAZOL-4-YL)ETHYL]AMINO}PYRIDO[2,3-D]PYRIMIDINE-6-CARBOXAMIDE
2
GOL
2
Ligand/Ion
GLYCEROL
3
NMN
1
Ligand/Ion
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
4
SO4
4
Ligand/Ion
SULFATE ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:120 , GLU A:175 , 3BA A:501 , HOH A:802 , HOH A:840
BINDING SITE FOR RESIDUE SO4 A 402
2
AC2
SOFTWARE
PRO A:81 , ARG A:129 , ARG A:137 , HOH A:647 , HOH A:832
BINDING SITE FOR RESIDUE SO4 A 403
3
AC3
SOFTWARE
ARG A:190 , GLN A:195 , GLN A:211 , ARG A:220 , HOH A:792 , HOH A:863
BINDING SITE FOR RESIDUE SO4 A 404
4
AC4
SOFTWARE
GLN A:24 , HIS A:27 , LYS A:32
BINDING SITE FOR RESIDUE SO4 A 405
5
AC5
SOFTWARE
TYR A:25 , TYR A:29 , TYR A:30 , VAL A:37 , ASP A:39 , TYR A:42 , ASP A:43 , ARG A:158 , HOH A:622 , HOH A:658 , HOH A:703 , HOH A:734 , HOH A:785
BINDING SITE FOR RESIDUE NMN A 401
6
AC6
SOFTWARE
TYR A:87 , LEU A:89 , GLU A:118 , LEU A:119 , LYS A:120 , ILE A:121 , GLU A:175 , TYR A:227 , VAL A:289 , LYS A:291 , TRP A:310 , SO4 A:402 , GOL A:603
BINDING SITE FOR RESIDUE 3BA A 501
7
AC7
SOFTWARE
PHE A:101 , ARG A:104 , ARG A:309 , HOH A:684 , HOH A:806
BINDING SITE FOR RESIDUE GOL A 602
8
AC8
SOFTWARE
PRO A:85 , MET A:86 , TYR A:87 , ARG A:173 , PHE A:303 , 3BA A:501 , HOH A:872
BINDING SITE FOR RESIDUE GOL A 603
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_LIGASE_N1 (A:120-149)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_LIGASE_N1
PS01055
NAD-dependent DNA ligase signature 1.
DNLJ_ENTFA
120-149
1
A:120-149
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3baaa_ (A:)
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(
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(
)
Folds
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(
)
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)
(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
DNA ligase/mRNA capping enzyme, catalytic domain
(33)
Family
:
Adenylation domain of NAD+-dependent DNA ligase
(16)
Protein domain
:
Adenylation domain of NAD+-dependent DNA ligase
(14)
Enterococcus faecalis [TaxId: 1351]
(9)
1a
d3baaa_
A:
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_3baaA03 (A:124-253)
2a: CATH_3baaA02 (A:88-122,A:254-317)
3a: CATH_3baaA01 (A:6-68)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
DNA ligase/mRNA capping enzyme
(18)
Streptococcus faecalis (Enterococcus faecalis)
(4)
1a
3baaA03
A:124-253
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.70, no name defined]
(15)
Streptococcus faecalis (Enterococcus faecalis)
(4)
2a
3baaA02
A:88-122,A:254-317
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
Streptococcus faecalis (Enterococcus faecalis)
(4)
3a
3baaA01
A:6-68
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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