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1ALZ
Asym. Unit
Info
Asym.Unit (39 KB)
Biol.Unit 1 (30 KB)
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(1)
Title
:
GRAMICIDIN D FROM BACILLUS BREVIS (ETHANOL SOLVATE)
Authors
:
B. M. Burkhart, W. A. Pangborn, W. L. Duax, D. A. Langs
Date
:
06 Jun 97 (Deposition) - 04 Mar 98 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
0.86
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Gramicidin, Antifungal, Antibiotic, Antibacterial, Membrane Ion Channel, Linear Gramicidin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. M. Burkhart, R. M. Gassman, D. A. Langs, W. A. Pangborn, W. L. Duax
Heterodimer Formation And Crystal Nucleation Of Gramicidin
Biophys. J. V. 75 2135 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 31)
Info
All Hetero Components
1a: D-LEUCINE (DLEa)
1b: D-LEUCINE (DLEb)
1c: D-LEUCINE (DLEc)
1d: D-LEUCINE (DLEd)
1e: D-LEUCINE (DLEe)
1f: D-LEUCINE (DLEf)
1g: D-LEUCINE (DLEg)
1h: D-LEUCINE (DLEh)
2a: D-VALINE (DVAa)
2b: D-VALINE (DVAb)
2c: D-VALINE (DVAc)
2d: D-VALINE (DVAd)
3a: ETHANOL (EOHa)
3b: ETHANOL (EOHb)
3c: ETHANOL (EOHc)
3d: ETHANOL (EOHd)
3e: ETHANOL (EOHe)
3f: ETHANOL (EOHf)
3g: ETHANOL (EOHg)
3h: ETHANOL (EOHh)
3i: ETHANOL (EOHi)
3j: ETHANOL (EOHj)
3k: ETHANOL (EOHk)
3l: ETHANOL (EOHl)
3m: ETHANOL (EOHm)
3n: ETHANOL (EOHn)
4a: ETHANOLAMINE (ETAa)
4b: ETHANOLAMINE (ETAb)
5a: N-FORMYL-L-VALINE (FVAa)
5b: N-FORMYL-L-VALINE (FVAb)
6a: N-FORMYL-L-ISOLEUCINE (QILa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DLE
8
Mod. Amino Acid
D-LEUCINE
2
DVA
4
Mod. Amino Acid
D-VALINE
3
EOH
14
Ligand/Ion
ETHANOL
4
ETA
2
Mod. Amino Acid
ETHANOLAMINE
5
FVA
2
Mod. Amino Acid
N-FORMYL-L-VALINE
6
QIL
1
Mod. Amino Acid
N-FORMYL-L-ISOLEUCINE
[
close Hetero Component info
]
Sites
(16, 16)
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:2 , EOH A:510 , EOH A:511 , EOH A:512 , DLE B:10
BINDING SITE FOR RESIDUE EOH A 501
02
AC2
SOFTWARE
DLE A:4 , EOH A:513 , EOH A:514 , TRP B:9 , TRP B:13 , TRP B:15 , ETA B:16 , EOH B:506
BINDING SITE FOR RESIDUE EOH A 504
03
AC3
SOFTWARE
TRP A:9 , TRP A:15 , ETA A:16 , EOH A:509 , EOH A:513 , TRP B:13
BINDING SITE FOR RESIDUE EOH A 505
04
AC4
SOFTWARE
DLE A:4 , TRP A:9 , DLE A:10 , DLE A:12 , EOH A:510
BINDING SITE FOR RESIDUE EOH A 507
05
AC5
SOFTWARE
VAL A:7 , DVA A:8 , TRP A:9 , TRP A:15 , EOH A:505 , DLE B:12
BINDING SITE FOR RESIDUE EOH A 509
06
AC6
SOFTWARE
TRP A:13 , EOH A:501 , EOH A:507 , EOH A:511
BINDING SITE FOR RESIDUE EOH A 510
07
AC7
SOFTWARE
TRP A:13 , DLE A:14 , EOH A:501 , EOH A:510 , EOH A:512 , HOH A:2001 , GLY B:2 , DLE B:10
BINDING SITE FOR RESIDUE EOH A 511
08
AC8
SOFTWARE
GLY A:2 , EOH A:501 , EOH A:511 , EOH A:514
BINDING SITE FOR RESIDUE EOH A 512
09
AC9
SOFTWARE
ETA A:16 , EOH A:504 , EOH A:505 , EOH A:514 , TRP B:13 , ETA B:16
BINDING SITE FOR RESIDUE EOH A 513
10
BC1
SOFTWARE
ALA A:5 , VAL A:7 , DVA A:8 , EOH A:504 , EOH A:512 , EOH A:513 , TRP B:9 , TRP B:11 , TRP B:13 , EOH B:506 , EOH B:508
BINDING SITE FOR RESIDUE EOH A 514
11
BC2
SOFTWARE
TRP A:15 , ETA A:16 , DLE B:4 , EOH B:508
BINDING SITE FOR RESIDUE EOH B 502
12
BC3
SOFTWARE
ETA A:16 , HOH A:2001 , TRP B:15
BINDING SITE FOR RESIDUE EOH B 503
13
BC4
SOFTWARE
TYR A:11 , ETA A:16 , EOH A:504 , EOH A:514 , TRP B:9 , DLE B:10 , EOH B:508
BINDING SITE FOR RESIDUE EOH B 506
14
BC5
SOFTWARE
EOH A:514 , TRP B:13 , EOH B:502 , EOH B:506
BINDING SITE FOR RESIDUE EOH B 508
15
BC6
SOFTWARE
EOH A:501 , EOH A:504 , EOH A:505 , EOH A:507 , EOH A:509 , EOH A:510 , EOH A:511 , EOH A:512 , EOH A:513 , EOH A:514 , HOH A:2001 , GLY B:2 , ALA B:3 , DLE B:4 , ALA B:5 , DVA B:6 , VAL B:7 , DVA B:8 , TRP B:9 , DLE B:10 , TRP B:11 , DLE B:12 , TRP B:13 , DLE B:14 , TRP B:15 , ETA B:16 , EOH B:502 , EOH B:503 , EOH B:506
BINDING SITE FOR CHAIN A OF ILE-GRAMICIDIN C
16
BC7
SOFTWARE
GLY A:2 , ALA A:3 , DLE A:4 , ALA A:5 , DVA A:6 , VAL A:7 , DVA A:8 , TRP A:9 , DLE A:10 , TYR A:11 , DLE A:12 , TRP A:13 , DLE A:14 , TRP A:15 , ETA A:16 , EOH A:501 , EOH A:504 , EOH A:505 , EOH A:507 , EOH A:509 , EOH A:511 , EOH A:512 , EOH A:513 , EOH A:514 , EOH B:502 , EOH B:503 , EOH B:506 , EOH B:508
BINDING SITE FOR CHAIN B OF VAL-GRAMICIDIN A
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1alza_ (A:)
1b: SCOP_d1alzb_ (B:)
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Protein Domains
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Organisms
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)
(
)
Class
:
Peptides
(792)
Fold
:
Membrane ion channel-forming peptide antibiotics containing D-aminoacids
(30)
Superfamily
:
Membrane ion channel-forming peptide antibiotics containing D-aminoacids
(30)
Family
:
Gramicidin
(21)
Protein domain
:
Gramicidin
(21)
Bacillus brevis [TaxId: 1393]
(21)
1a
d1alza_
A:
1b
d1alzb_
B:
[
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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
(0, 0)
Info
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Sorry, no Info available
[
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Atom Selection
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Protein
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Ligand
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
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Miscellaneous
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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)
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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") .
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Asym.Unit (39 KB)
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Header - Biol.Unit 1
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