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5DCC
Asym. Unit
Info
Asym.Unit (245 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (121 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF A TEBIPENEM ADDUCT OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
Authors
:
Y. Pan, L. Basta, G. Lamichhane, M. A. Bianchet
Date
:
23 Aug 15 (Deposition) - 28 Sep 16 (Release) - 28 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
L, D -Transpeptidase, Carbapenems Tebipenem-Adduct, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Pan, L. A. Basta, H. Saavedra, R. Mattoo, K. Pankaj, E. P. Lloyd, C. A. Townsend, M. A. Bianchet, G. Lamichhane
Molecular Structures And Mechanism Of Inhibition Of Mycobacterium Tuberculosis L, D-Transpeptidase By Tebipenem And Biapenem
To Be Published
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(6, 33)
Info
All Hetero Components
1a: (4S)-4-METHYL-2,5,7-TRIOXOHEPTANOI... (58Ua)
1b: (4S)-4-METHYL-2,5,7-TRIOXOHEPTANOI... (58Ub)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
4e: DI(HYDROXYETHYL)ETHER (PEGe)
4f: DI(HYDROXYETHYL)ETHER (PEGf)
4g: DI(HYDROXYETHYL)ETHER (PEGg)
4h: DI(HYDROXYETHYL)ETHER (PEGh)
4i: DI(HYDROXYETHYL)ETHER (PEGi)
5a: TRIETHYLENE GLYCOL (PGEa)
5b: TRIETHYLENE GLYCOL (PGEb)
5c: TRIETHYLENE GLYCOL (PGEc)
5d: TRIETHYLENE GLYCOL (PGEd)
5e: TRIETHYLENE GLYCOL (PGEe)
5f: TRIETHYLENE GLYCOL (PGEf)
5g: TRIETHYLENE GLYCOL (PGEg)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
6i: SULFATE ION (SO4i)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
58U
2
Ligand/Ion
(4S)-4-METHYL-2,5,7-TRIOXOHEPTANOIC ACID
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
4
Ligand/Ion
GLYCEROL
4
PEG
9
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PGE
7
Ligand/Ion
TRIETHYLENE GLYCOL
6
SO4
9
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(33, 33)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:303 , TYR A:318 , GLY A:332 , HIS A:336 , TRP A:340 , SER A:351 , HIS A:352 , GLY A:353 , CYS A:354 , ASN A:356 , EDO A:516 , HOH A:604 , HOH A:715
binding site for residue 58U A 501
02
AC2
SOFTWARE
ARG A:99 , ARG A:122 , SO4 A:506 , HOH A:641 , PRO B:311 , VAL B:312 , ASN B:313 , HOH B:649
binding site for residue SO4 A 502
03
AC3
SOFTWARE
GLU A:162 , ARG A:371 , HOH A:611 , HOH A:621
binding site for residue SO4 A 503
04
AC4
SOFTWARE
MET A:157 , ARG A:209 , TYR A:330 , ARG A:371 , HOH A:728
binding site for residue SO4 A 504
05
AC5
SOFTWARE
ARG A:104 , SER A:106 , PRO A:107 , ARG A:111 , HOH A:605 , HOH A:713
binding site for residue SO4 A 505
06
AC6
SOFTWARE
ASN A:95 , ARG A:99 , ARG A:122 , SO4 A:502 , SER B:306 , PRO B:311
binding site for residue SO4 A 506
07
AC7
SOFTWARE
ASN A:204 , ASN A:205 , HOH A:607
binding site for residue PEG A 507
08
AC8
SOFTWARE
GLU A:185 , ALA A:199 , PHE A:200 , TRP A:401 , ARG A:402 , GLY A:404 , PEG A:509 , HOH A:654 , HOH A:690
binding site for residue PEG A 508
09
AC9
SOFTWARE
ILE A:188 , ILE A:190 , GLY A:198 , TRP A:210 , PEG A:508 , PGE A:511 , HOH A:734
binding site for residue PEG A 509
10
AD1
SOFTWARE
HIS A:214 , PHE A:215 , LYS B:186
binding site for residue PGE A 510
11
AD2
SOFTWARE
LYS A:189 , ILE A:190 , THR A:192 , VAL A:196 , TRP A:210 , PEG A:509 , HOH A:657
binding site for residue PGE A 511
12
AD3
SOFTWARE
VAL A:91 , THR A:92 , MET A:93 , VAL A:101 , GLY A:103 , TRP A:112
binding site for residue PGE A 512
13
AD4
SOFTWARE
THR A:256 , ASP A:258 , THR A:261 , ILE A:263 , THR A:265 , HOH A:606 , HOH A:618 , VAL B:196 , GLU B:197 , GLY B:198 , TRP B:210 , PEG B:506
binding site for residue PGE A 513
14
AD5
SOFTWARE
ARG A:181 , TRP A:202 , LEU A:203 , ASN A:205 , ASN A:405 , HOH A:607
binding site for residue GOL A 514
15
AD6
SOFTWARE
VAL A:75 , ASP A:76 , ALA A:77 , PRO A:78 , GLN A:117 , LEU A:118
binding site for residue GOL A 515
16
AD7
SOFTWARE
TYR A:318 , SER A:331 , 58U A:501 , HOH A:691
binding site for residue EDO A 516
17
AD8
SOFTWARE
ARG B:297 , ARG B:371 , PEG B:510 , HOH B:604 , HOH B:643
binding site for residue SO4 B 502
18
AD9
SOFTWARE
PRO A:311 , VAL A:312 , ASN A:313 , ARG B:122 , SO4 B:504
binding site for residue SO4 B 503
19
AE1
SOFTWARE
SER A:306 , PRO A:311 , ASN B:95 , ASN B:97 , ARG B:99 , ARG B:122 , SO4 B:503
binding site for residue SO4 B 504
20
AE2
SOFTWARE
ARG B:104 , PRO B:107 , ARG B:111 , HOH B:714
binding site for residue SO4 B 505
21
AE3
SOFTWARE
PGE A:513 , ILE B:188 , LYS B:189 , ILE B:190
binding site for residue PEG B 506
22
AE4
SOFTWARE
VAL A:71 , HIS B:214 , HOH B:605
binding site for residue PEG B 507
23
AE5
SOFTWARE
LEU B:385 , GLY B:387 , ILE B:396 , PGE B:514 , HOH B:733
binding site for residue PEG B 508
24
AE6
SOFTWARE
ASP B:251 , HIS B:368
binding site for residue PEG B 509
25
AE7
SOFTWARE
MET B:157 , PRO B:158 , GLY B:159 , GLU B:162 , VAL B:164 , ARG B:371 , SO4 B:502
binding site for residue PEG B 510
26
AE8
SOFTWARE
ALA B:183 , LYS B:186 , ALA B:187 , VAL B:231 , ASP B:232
binding site for residue PEG B 511
27
AE9
SOFTWARE
GLU B:376 , TRP B:394 , ASN B:395 , HOH B:621
binding site for residue PGE B 512
28
AF1
SOFTWARE
GLU B:168 , PRO B:169 , GLY B:295 , SER B:296 , GLN B:327 , TYR B:330 , ARG B:371
binding site for residue PGE B 513
29
AF2
SOFTWARE
ARG B:181 , TYR B:201 , TRP B:202 , LEU B:203 , ILE B:388 , ASN B:405 , PEG B:508 , HOH B:642 , HOH B:688 , HOH B:699
binding site for residue PGE B 514
30
AF3
SOFTWARE
GLU B:213 , HIS B:214 , PHE B:215 , ILE B:291 , TRP B:394
binding site for residue GOL B 515
31
AF4
SOFTWARE
ALA B:90 , VAL B:91 , LEU B:105
binding site for residue GOL B 516
32
AF5
SOFTWARE
TYR B:318 , SER B:331 , GLY B:353 , 58U B:501
binding site for residue EDO B 517
33
AF6
SOFTWARE
SER B:279 , MET B:280 , TYR B:318 , GLY B:332 , PHE B:334 , HIS B:336 , TRP B:340 , SER B:351 , HIS B:352 , GLY B:353 , LEU B:355 , ASN B:356 , EDO B:517 , HOH B:697
binding site for Di-peptide 58U B 501 and CYS B 354
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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