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Getting 'Exon' information from database.
3PED
Asym. Unit
Info
Asym.Unit (96 KB)
Biol.Unit 1 (32 KB)
Biol.Unit 2 (31 KB)
Biol.Unit 3 (33 KB)
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(1)
Title
:
SIDEROCALIN RECOGNITIN OF CARBOXYMYCOBACTINS: INTERFERENCE BY THE IMMUNE SYSTEM IN INTRACELLULAR IRON ACQUISITION BY MYCOBACTERIA TUBERCULOSIS
Authors
:
M. C. Clifton
Date
:
25 Oct 10 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
8-Stranded Anti-Parallel Beta Barrel, Siderocalin, Siderophore Binding, Antimicrobial Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. M. Hoette, M. C. Clifton, A. M. Zawadzka, M. A. Holmes, R. K. Strong, K. R. Raymond
Siderocalin Recognitin Of Carboxymycobactins: Interference By The Immune System In Intracellular Iron Acquisition By Mycobacteria Tuberculosis
To Be Published
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
2a: SULFATE ION (SO4a)
3a: (9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{... (ZYFa)
3b: (9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{... (ZYFb)
3c: (9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{... (ZYFc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
3
Ligand/Ion
FE (III) ION
2
SO4
1
Ligand/Ion
SULFATE ION
3
ZYF
3
Ligand/Ion
(9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{[(3S)-1-HYDROXY-2-OXOAZEPAN-3-YL]AMINO}-1-METHYL-3-OXOPROPYL]OXY}-5-({[(4S)-2-(2-HYDROXYPHENYL)-4,5-DIHYDRO-1,3-OXAZOL-4-YL]CARBONYL}AMINO)-6-OXOHEXYL]AMINO}-11-OXOUNDEC-9-ENOIC ACID
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ZYF A:200
BINDING SITE FOR RESIDUE FE A 179
2
AC2
SOFTWARE
TYR A:52 , THR A:54 , VAL A:66 , SER A:68 , LEU A:70 , TRP A:79 , ARG A:81 , PHE A:123 , LYS A:125 , LYS A:134 , TYR A:138 , FE A:179 , HOH A:182 , HOH A:223
BINDING SITE FOR RESIDUE ZYF A 200
3
AC3
SOFTWARE
ZYF B:200
BINDING SITE FOR RESIDUE FE B 179
4
AC4
SOFTWARE
TYR B:52 , THR B:54 , SER B:68 , TRP B:79 , ARG B:81 , PHE B:83 , LYS B:125 , PHE B:133 , LYS B:134 , TYR B:138 , FE B:179 , HOH B:184 , HOH B:196 , HOH B:197
BINDING SITE FOR RESIDUE ZYF B 200
5
AC5
SOFTWARE
ZYF C:200
BINDING SITE FOR RESIDUE FE C 179
6
AC6
SOFTWARE
TYR C:52 , THR C:54 , SER C:68 , LEU C:70 , TRP C:79 , PHE C:123 , LYS C:125 , PHE C:133 , LYS C:134 , TYR C:138 , FE C:179
BINDING SITE FOR RESIDUE ZYF C 200
7
AC7
SOFTWARE
GLN A:117 , ASN C:114 , HOH C:246 , HOH C:252
BINDING SITE FOR RESIDUE SO4 C 180
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: LIPOCALIN (A:21-34,B:21-34,C:21-34)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LIPOCALIN
PS00213
Lipocalin signature.
NGAL_HUMAN
41-54
3
A:21-34
B:21-34
C:21-34
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Exons
(6, 18)
Info
All Exons
Exon 1.2d (A:2-26 | B:5-26 | C:6-26)
Exon 1.3 (A:27-72 | B:27-72 (gaps) | C:27-72)
Exon 1.6b (A:72-99 | B:72-99 | C:72-99)
Exon 1.7 (A:99-139 | B:99-139 | C:99-139)
Exon 1.8 (A:139-173 | B:139-173 | C:139-173)
Exon 1.9b (A:173-178 | B:173-177 | C:173-177)
View:
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All Exon Boundaries
1: Boundary 1.1/1.2d
2: Boundary 1.2d/1.3
3: Boundary 1.3/1.6b
4: Boundary 1.6b/1.7
5: Boundary 1.7/1.8
6: Boundary 1.8/1.9b
7: Boundary 1.9b/-
View:
Label:
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
ENST00000373017
1
ENSE00001459333
chr9:
130911350-130911543
194
NGAL_HUMAN
-
0
0
-
-
1.2d
ENST00000373017
2d
ENSE00001459332
chr9:
130911762-130911942
181
NGAL_HUMAN
1-46
46
3
A:2-26
B:5-26
C:6-26
25
22
21
1.3
ENST00000373017
3
ENSE00000984625
chr9:
130912517-130912653
137
NGAL_HUMAN
47-92
46
3
A:27-72
B:27-72 (gaps)
C:27-72
46
46
46
1.6b
ENST00000373017
6b
ENSE00000984626
chr9:
130913917-130913996
80
NGAL_HUMAN
92-119
28
3
A:72-99
B:72-99
C:72-99
28
28
28
1.7
ENST00000373017
7
ENSE00000984627
chr9:
130914185-130914304
120
NGAL_HUMAN
119-159
41
3
A:99-139
B:99-139
C:99-139
41
41
41
1.8
ENST00000373017
8
ENSE00001419823
chr9:
130914462-130914563
102
NGAL_HUMAN
159-193
35
3
A:139-173
B:139-173
C:139-173
35
35
35
1.9b
ENST00000373017
9b
ENSE00001459311
chr9:
130915379-130915412
34
NGAL_HUMAN
193-198
6
3
A:173-178
B:173-177
C:173-177
6
5
5
[
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SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3peda_ (A:)
1b: SCOP_d3pedb_ (B:)
1c: SCOP_d3pedc_ (C:)
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Protein Domains
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Organisms
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(
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Class
:
All beta proteins
(24004)
Fold
:
Lipocalins
(514)
Superfamily
:
Lipocalins
(514)
Family
:
Retinol binding protein-like
(261)
Protein domain
:
Neutrophil gelatinase-associated lipocalin (NGAL)
(28)
Human (Homo sapiens) [TaxId: 9606]
(28)
1a
d3peda_
A:
1b
d3pedb_
B:
1c
d3pedc_
C:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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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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Protein & NOT PROSITE
Chain A
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Chain C
Asymmetric Unit 1
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Example Commands
Example Command
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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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Show PDB file:
Asym.Unit (96 KB)
Header - Asym.Unit
Biol.Unit 1 (32 KB)
Header - Biol.Unit 1
Biol.Unit 2 (31 KB)
Header - Biol.Unit 2
Biol.Unit 3 (33 KB)
Header - Biol.Unit 3
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