PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
5DC2
Asym. Unit
Info
Asym.Unit (257 KB)
Biol.Unit 1 (126 KB)
Biol.Unit 2 (128 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
Authors
:
Y. Pan, L. Basta, G. Lamichhane, M. A. Bianchet
Date
:
23 Aug 15 (Deposition) - 05 Oct 16 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.18
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
L, D-Transpeptidase, Carbapenems Biapenem-Adduct, Ldtmt2, Mycobacterium Tuberculosis, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. A. Bianchet, Y. H. Pan, L. A. B. Basta, H. Saavedra, E. P. Lloyd, P. Kumar, R. Mattoo, C. A. Townsend, G. Lamichhane
Structural Insight Into The Inactivation Of Mycobacterium Tuberculosis Non-Classical Transpeptidase Ldtmt2 By Biapene And Tebipenem.
Bmc Biochem. V. 18 8 2017
(for further references see the
PDB file header
)
[
close entry info
]
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)
3e: GLYCEROL (GOLe)
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)
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)
6j: SULFATE ION (SO4j)
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
5
Ligand/Ion
GLYCEROL
4
PEG
9
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PGE
5
Ligand/Ion
TRIETHYLENE GLYCOL
6
SO4
10
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:606 , HOH A:625
binding site for residue 58U A 501
02
AC2
SOFTWARE
ARG A:122 , SO4 A:506 , HOH A:601 , HOH A:656 , PRO B:311 , VAL B:312 , ASN B:313 , HOH B:641
binding site for residue SO4 A 502
03
AC3
SOFTWARE
ARG A:371 , HOH A:626 , HOH A:652 , HOH A:695 , HOH A:758
binding site for residue SO4 A 503
04
AC4
SOFTWARE
MET A:157 , TYR A:330 , ARG A:371 , HOH A:605
binding site for residue SO4 A 504
05
AC5
SOFTWARE
SER A:106 , PRO A:107 , ARG A:111 , HOH A:628 , HOH A:703
binding site for residue SO4 A 505
06
AC6
SOFTWARE
ASN A:95 , ARG A:99 , SO4 A:502 , HOH A:601 , HOH A:619 , SER B:306
binding site for residue SO4 A 506
07
AC7
SOFTWARE
ASN A:204 , ASN A:205 , HOH A:761
binding site for residue PEG A 507
08
AC8
SOFTWARE
GLY A:86 , LEU A:131 , GLY A:132 , HOH A:615
binding site for residue PEG A 508
09
AC9
SOFTWARE
GLU A:185 , ALA A:199 , PHE A:200 , TRP A:401 , ARG A:402 , GLY A:404 , PEG A:510 , HOH A:688
binding site for residue PEG A 509
10
AD1
SOFTWARE
ILE A:188 , LYS A:189 , ILE A:190 , GLY A:198 , TRP A:210 , PEG A:509 , HOH A:750
binding site for residue PEG A 510
11
AD2
SOFTWARE
HIS A:214 , PHE A:215 , GLU A:252 , ILE A:254 , HOH A:638 , LYS B:186
binding site for residue PGE A 511
12
AD3
SOFTWARE
LYS A:189 , ILE A:190 , THR A:192 , VAL A:196 , HOH A:719 , ASN B:260
binding site for residue PGE A 512
13
AD4
SOFTWARE
ARG A:123 , THR A:142 , SER A:358 , PRO A:359 , SER A:360 , HOH A:603 , HOH A:714
binding site for residue GOL A 513
14
AD5
SOFTWARE
ARG A:181 , TRP A:202 , LEU A:203 , HOH A:608 , HOH A:621
binding site for residue GOL A 514
15
AD6
SOFTWARE
VAL A:75 , ALA A:77 , PRO A:78 , GLN A:117 , LEU A:118 , HOH A:763
binding site for residue GOL A 515
16
AD7
SOFTWARE
TYR A:318 , SER A:331 , HIS A:352 , GLY A:353 , 58U A:501
binding site for residue EDO A 516
17
AD8
SOFTWARE
ARG B:297 , ARG B:371 , HOH B:621 , HOH B:681
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 , HOH B:616 , HOH B:623 , HOH B:749
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 , SO4 B:503 , HOH B:658
binding site for residue SO4 B 504
20
AE2
SOFTWARE
ARG B:104 , SER B:106 , PRO B:107 , ARG B:111 , HOH B:630 , HOH B:748
binding site for residue SO4 B 505
21
AE3
SOFTWARE
LEU A:62 , ARG A:139 , LEU A:141 , ASP B:399 , HOH B:609 , HOH B:622
binding site for residue PEG B 507
22
AE4
SOFTWARE
ILE B:190 , TRP B:210
binding site for residue PEG B 508
23
AE5
SOFTWARE
VAL A:71 , HOH A:843 , GLU B:213 , HIS B:214
binding site for residue PEG B 509
24
AE6
SOFTWARE
PRO B:386 , GLY B:387 , GLN B:400 , PGE B:514 , HOH B:610 , HOH B:613
binding site for residue PEG B 510
25
AE7
SOFTWARE
ASP B:251 , HIS B:368 , HOH B:611 , HOH B:635
binding site for residue PEG B 511
26
AE8
SOFTWARE
GLU B:376 , VAL B:378 , PRO B:397 , GOL B:515 , HOH B:603 , HOH B:763
binding site for residue PGE B 512
27
AE9
SOFTWARE
GLU B:168 , PRO B:169 , ALA B:171 , GLY B:295 , SER B:296 , GLN B:327 , TYR B:330 , ARG B:371
binding site for residue PGE B 513
28
AF1
SOFTWARE
ARG B:181 , TYR B:201 , TRP B:202 , ILE B:388 , ASN B:405 , ALA B:408 , PEG B:510 , HOH B:610
binding site for residue PGE B 514
29
AF2
SOFTWARE
GLU B:213 , HIS B:214 , PHE B:215 , ILE B:291 , PGE B:512 , HOH B:750
binding site for residue GOL B 515
30
AF3
SOFTWARE
ALA B:90 , VAL B:91 , LEU B:105 , TRP B:112
binding site for residue GOL B 516
31
AF4
SOFTWARE
TYR B:318 , SER B:331 , GLY B:332 , 58U B:501
binding site for residue EDO B 517
32
AF5
SOFTWARE
SER B:279 , MET B:280 , MET B:303 , 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:612
binding site for Di-peptide 58U B 501 and CYS B 354
33
AF6
SOFTWARE
ASN B:95 , ASP B:96 , ARG B:122 , TYR B:124 , PHE B:143 , GLN B:144 , SER B:358 , SER B:360 , HOH B:605 , HOH B:638 , HOH B:732
binding site for Di-peptide SO4 B 506 and ARG B 123
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (257 KB)
Header - Asym.Unit
Biol.Unit 1 (126 KB)
Header - Biol.Unit 1
Biol.Unit 2 (128 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
5DC2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
