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3RUL
Asym. Unit
Info
Asym.Unit (76 KB)
Biol.Unit 1 (20 KB)
Biol.Unit 2 (20 KB)
Biol.Unit 3 (20 KB)
Biol.Unit 4 (20 KB)
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(1)
Title
:
NEW STRATEGY TO ANALYZE STRUCTURES OF GLYCOPEPTIDE-TARGET COMPLEXES
Authors
:
N. J. Economou, V. Nahoum, S. D. Weeks, K. C. Grasty, P. J. Loll
Date
:
05 May 11 (Deposition) - 06 Jun 12 (Release) - 06 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,G (1x)
Biol. Unit 4: D,H (1x)
Keywords
:
Antibiotic, Glycopeptide, Native Protein Ligation, Fusion, Carboxymethylation Of Cysteine, Dalbavancin, Signaling Protein- Antibiotic Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. J. Economou, V. Nahoum, S. D. Weeks, K. C. Grasty, I. J. Zentner, T. M. Townsend, M. W. Bhuiya, S. Cocklin, P. J. Loll
A Carrier Protein Strategy Yields The Structure Of Dalbavancin.
J. Am. Chem. Soc. V. 134 4637 2012
[
close entry info
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Hetero Components
(13, 57)
Info
All Hetero Components
01a: CARBOXYMETHYLATED CYSTEINE (CCSa)
01b: CARBOXYMETHYLATED CYSTEINE (CCSb)
01c: CARBOXYMETHYLATED CYSTEINE (CCSc)
01d: CARBOXYMETHYLATED CYSTEINE (CCSd)
02a: CHLORIDE ION (CLa)
03a: D-ALANINE (DALa)
03b: D-ALANINE (DALb)
03c: D-ALANINE (DALc)
03d: D-ALANINE (DALd)
03e: D-ALANINE (DALe)
03f: D-ALANINE (DALf)
03g: D-ALANINE (DALg)
03h: D-ALANINE (DALh)
04a: D-TYROSINE (DTYa)
04b: D-TYROSINE (DTYb)
04c: D-TYROSINE (DTYc)
04d: D-TYROSINE (DTYd)
05a: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPa)
05b: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPb)
05c: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPc)
05d: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPd)
05e: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPe)
05f: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPf)
05g: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPg)
05h: (2R)-AMINO(4-HYDROXYPHENYL)ETHANOI... (GHPh)
06a: (2S)-2-AZANYL-2-[2-CHLORANYL-3,5-B... (HCLa)
06b: (2S)-2-AZANYL-2-[2-CHLORANYL-3,5-B... (HCLb)
06c: (2S)-2-AZANYL-2-[2-CHLORANYL-3,5-B... (HCLc)
06d: (2S)-2-AZANYL-2-[2-CHLORANYL-3,5-B... (HCLd)
07a: (2S)-2-AZANYL-N-[3-(DIMETHYLAMINO)... (HG7a)
07b: (2S)-2-AZANYL-N-[3-(DIMETHYLAMINO)... (HG7b)
07c: (2S)-2-AZANYL-N-[3-(DIMETHYLAMINO)... (HG7c)
07d: (2S)-2-AZANYL-N-[3-(DIMETHYLAMINO)... (HG7d)
08a: (2R)-2-(4-HYDROXYPHENYL)-2-(METHYL... (HGMa)
08b: (2R)-2-(4-HYDROXYPHENYL)-2-(METHYL... (HGMb)
08c: (2R)-2-(4-HYDROXYPHENYL)-2-(METHYL... (HGMc)
08d: (2R)-2-(4-HYDROXYPHENYL)-2-(METHYL... (HGMd)
09a: 10-METHYLUNDECANOIC ACID (M12a)
09b: 10-METHYLUNDECANOIC ACID (M12b)
09c: 10-METHYLUNDECANOIC ACID (M12c)
09d: 10-METHYLUNDECANOIC ACID (M12d)
10a: ALPHA-D-MANNOSE (MANa)
10b: ALPHA-D-MANNOSE (MANb)
10c: ALPHA-D-MANNOSE (MANc)
10d: ALPHA-D-MANNOSE (MANd)
11a: 2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANU... (N1La)
11b: 2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANU... (N1Lb)
11c: 2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANU... (N1Lc)
11d: 2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANU... (N1Ld)
12a: (BETAR)-3-CHLORO-BETA-HYDROXY-L-TY... (OMYa)
12b: (BETAR)-3-CHLORO-BETA-HYDROXY-L-TY... (OMYb)
12c: (BETAR)-3-CHLORO-BETA-HYDROXY-L-TY... (OMYc)
12d: (BETAR)-3-CHLORO-BETA-HYDROXY-L-TY... (OMYd)
13a: L(+)-TARTARIC ACID (TLAa)
13b: L(+)-TARTARIC ACID (TLAb)
13c: L(+)-TARTARIC ACID (TLAc)
13d: L(+)-TARTARIC ACID (TLAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CCS
4
Mod. Amino Acid
CARBOXYMETHYLATED CYSTEINE
2
CL
1
Ligand/Ion
CHLORIDE ION
3
DAL
8
Mod. Amino Acid
D-ALANINE
4
DTY
4
OTHER
D-TYROSINE
5
GHP
8
OTHER
(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
6
HCL
4
OTHER
(2S)-2-AZANYL-2-[2-CHLORANYL-3,5-BIS(OXIDANYL)PHENYL]ETHANOIC ACID
7
HG7
4
OTHER
(2S)-2-AZANYL-N-[3-(DIMETHYLAMINO)PROPYL]-2-(3-HYDROXYPHENYL)ETHANAMIDE
8
HGM
4
OTHER
(2R)-2-(4-HYDROXYPHENYL)-2-(METHYLAMINO)ETHANOIC ACID
9
M12
4
Ligand/Ion
10-METHYLUNDECANOIC ACID
10
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
11
N1L
4
Ligand/Ion
2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANURONIC ACID
12
OMY
4
OTHER
(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
13
TLA
4
Ligand/Ion
L(+)-TARTARIC ACID
[
close Hetero Component info
]
Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:42 , GLN A:49 , ARG A:72 , ARG D:74 , N1L H:8 , M12 H:10
BINDING SITE FOR RESIDUE TLA A 101
2
AC2
SOFTWARE
THR A:9 , LYS A:11 , LYS D:33 , HGM G:1 , HCL G:3
BINDING SITE FOR RESIDUE TLA A 102
3
AC3
SOFTWARE
ARG B:74 , ARG C:42 , ARG C:72 , N1L F:8 , M12 F:10
BINDING SITE FOR RESIDUE TLA B 101
4
AC4
SOFTWARE
ARG B:42 , ARG B:72 , ARG C:74 , M12 G:10
BINDING SITE FOR RESIDUE TLA B 102
5
AC5
SOFTWARE
LYS B:27 , ARG B:42 , GLN B:49
BINDING SITE FOR RESIDUE CL B 103
6
AC6
SOFTWARE
GLY A:75 , LYS A:77 , DAL A:78 , DAL A:79 , GLU B:16 , LYS B:29 , ASP B:32 , LYS B:33 , LEU C:8 , THR C:9 , GLN C:40 , LEU C:69 , VAL C:70 , LEU C:71 , ARG C:72 , LEU C:73 , HOH C:101 , ILE D:44 , GLY D:47 , GLN D:49 , ARG D:72 , M12 F:10
BINDING SITE FOR CHAIN E OF DALBAVANCIN
7
AC7
SOFTWARE
GLY B:75 , LYS B:77 , DAL B:78 , DAL B:79 , TLA B:101 , ILE C:44 , GLY C:47 , GLN C:49 , VAL C:70 , ARG C:72 , LEU D:8 , THR D:9 , GLN D:40 , LEU D:69 , VAL D:70 , LEU D:71 , ARG D:72 , LEU D:73 , HOH D:101 , HOH D:102 , M12 E:10
BINDING SITE FOR CHAIN F OF DALBAVANCIN
8
AC8
SOFTWARE
LEU A:8 , THR A:9 , GLN A:40 , LEU A:69 , VAL A:70 , LEU A:71 , ARG A:72 , LEU A:73 , TLA A:102 , HOH A:203 , ILE B:44 , GLY B:47 , GLN B:49 , ARG B:72 , TLA B:102 , GLY C:75 , LYS C:77 , DAL C:78 , DAL C:79 , HOH G:201 , M12 H:10
BINDING SITE FOR CHAIN G OF DALBAVANCIN
9
AC9
SOFTWARE
ILE A:44 , GLY A:47 , GLN A:49 , ARG A:72 , TLA A:101 , LEU B:8 , THR B:9 , GLN B:40 , LEU B:69 , VAL B:70 , LEU B:71 , ARG B:72 , LEU B:73 , HOH B:202 , GLY D:75 , LYS D:77 , DAL D:78 , DAL D:79 , M12 G:10 , HOH H:201 , HOH H:202
BINDING SITE FOR CHAIN H OF DALBAVANCIN
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (-|-|-|-|-|-|-|A:1-75,B:1-75,C:1-75...)
2: UBIQUITIN_1 (-|-|-|-|-|-|-|A:27-52,B:27-52,C:27...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
8
-
-
-
-
-
-
-
A:1-75
B:1-75
C:1-75
D:1-75
A:77-77
B:77-77
C:77-77
D:77-77
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
4
-
-
-
-
-
-
-
A:27-52
B:27-52
C:27-52
D:27-52
-
[
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]
Exons
(1, 4)
Info
All Exons
Exon 1.2 (A:1-79 (gaps) | B:1-79 (gaps) | C:...)
View:
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000339647
1
ENSE00001257182
chr12:
125399577-125399133
445
UBC_HUMAN
-
0
0
-
-
1.2
ENST00000339647
2
ENSE00001406973
chr12:
125398320-125396194
2127
UBC_HUMAN
1-686
686
4
A:1-79 (gaps)
B:1-79 (gaps)
C:1-79 (gaps)
D:1-79 (gaps)
84
84
84
84
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3rula_ (A:)
1b: SCOP_d3rulb_ (B:)
1c: SCOP_d3rulc_ (C:)
1d: SCOP_d3ruld_ (D:)
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(
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(
)
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(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ubiquitin-related
(337)
Protein domain
:
Ubiquitin
(162)
Human (Homo sapiens) [TaxId: 9606]
(121)
1a
d3rula_
A:
1b
d3rulb_
B:
1c
d3rulc_
C:
1d
d3ruld_
D:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
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