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3U0D
Asym. Unit
Info
Asym.Unit (246 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (61 KB)
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(1)
Title
:
THE STRUCTURE OF HUMAN SIDEROCALIN BOUND TO THE BACTERIAL SIDEROPHORE 2,3-DHBA
Authors
:
Seattle Structural Genomics Center For Infectious Disease (S
Date
:
28 Sep 11 (Deposition) - 12 Oct 11 (Release) - 09 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.51
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Siderophore, Beta-Barrel, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Transport Protein, Antimicrobial Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Correnti, V. Richardson, A. K. Sia, A. D. Bandaranayake, M. Ruiz, Y. Suryo Rahmanto, Z. Kovacevic, M. C. Clifton, M. A. Holmes, B. K. Kaiser, J. Barasch, K. N. Raymond, D. R. Richardson, R. K. Strong
Siderocalin/Lcn2/Ngal/24P3 Does Not Drive Apoptosis Through Gentisic Acid Mediated Iron Withdrawal In Hematopoietic Cel Lines.
Plos One V. 7 43696 2012
[
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Hetero Components
(3, 19)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: 2,3-DIHYDROXY-BENZOIC ACID (DBHa)
2b: 2,3-DIHYDROXY-BENZOIC ACID (DBHb)
2c: 2,3-DIHYDROXY-BENZOIC ACID (DBHc)
2d: 2,3-DIHYDROXY-BENZOIC ACID (DBHd)
2e: 2,3-DIHYDROXY-BENZOIC ACID (DBHe)
2f: 2,3-DIHYDROXY-BENZOIC ACID (DBHf)
2g: 2,3-DIHYDROXY-BENZOIC ACID (DBHg)
2h: 2,3-DIHYDROXY-BENZOIC ACID (DBHh)
2i: 2,3-DIHYDROXY-BENZOIC ACID (DBHi)
2j: 2,3-DIHYDROXY-BENZOIC ACID (DBHj)
2k: 2,3-DIHYDROXY-BENZOIC ACID (DBHk)
2l: 2,3-DIHYDROXY-BENZOIC ACID (DBHl)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
3d: FE (III) ION (FEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
3
Ligand/Ion
CHLORIDE ION
2
DBH
12
Ligand/Ion
2,3-DIHYDROXY-BENZOIC ACID
3
FE
4
Ligand/Ion
FE (III) ION
[
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]
Sites
(19, 19)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
DBH A:180 , DBH A:181 , DBH A:182
BINDING SITE FOR RESIDUE FE A 179
02
AC2
SOFTWARE
SER A:68 , ARG A:72 , TRP A:79 , ARG A:81 , LYS A:134 , FE A:179 , DBH A:181 , DBH A:182
BINDING SITE FOR RESIDUE DBH A 180
03
AC3
SOFTWARE
TRP A:79 , ARG A:81 , LEU A:94 , LEU A:103 , TYR A:106 , LYS A:125 , FE A:179 , DBH A:180 , DBH A:182
BINDING SITE FOR RESIDUE DBH A 181
04
AC4
SOFTWARE
TYR A:106 , LYS A:125 , LYS A:134 , FE A:179 , DBH A:180 , DBH A:181 , HOH A:185 , HOH A:187
BINDING SITE FOR RESIDUE DBH A 182
05
AC5
SOFTWARE
DBH D:180 , DBH D:181 , DBH D:182
BINDING SITE FOR RESIDUE FE D 179
06
AC6
SOFTWARE
SER D:68 , TRP D:79 , LYS D:134 , FE D:179 , DBH D:181 , DBH D:182
BINDING SITE FOR RESIDUE DBH D 180
07
AC7
SOFTWARE
TRP D:79 , ARG D:81 , TYR D:100 , TYR D:106 , LYS D:125 , FE D:179 , DBH D:180 , DBH D:182
BINDING SITE FOR RESIDUE DBH D 181
08
AC8
SOFTWARE
TYR D:106 , LYS D:125 , LYS D:134 , FE D:179 , DBH D:180 , DBH D:181 , HOH D:185 , HOH D:197
BINDING SITE FOR RESIDUE DBH D 182
09
AC9
SOFTWARE
DBH B:180 , DBH B:181 , DBH B:182
BINDING SITE FOR RESIDUE FE B 179
10
BC1
SOFTWARE
TRP B:79 , ARG B:81 , TYR B:106 , LYS B:125 , FE B:179 , DBH B:181 , DBH B:182 , HOH B:214 , HOH B:217
BINDING SITE FOR RESIDUE DBH B 180
11
BC2
SOFTWARE
ALA B:40 , TYR B:106 , LYS B:134 , FE B:179 , DBH B:180 , DBH B:182 , HOH B:187
BINDING SITE FOR RESIDUE DBH B 181
12
BC3
SOFTWARE
ARG B:72 , TRP B:79 , LYS B:134 , FE B:179 , DBH B:180 , DBH B:181 , HOH B:214
BINDING SITE FOR RESIDUE DBH B 182
13
BC4
SOFTWARE
DBH C:180 , DBH C:181 , DBH C:182
BINDING SITE FOR RESIDUE FE C 179
14
BC5
SOFTWARE
ARG C:72 , TRP C:79 , LYS C:134 , FE C:179 , DBH C:181 , DBH C:182 , HOH C:202
BINDING SITE FOR RESIDUE DBH C 180
15
BC6
SOFTWARE
TRP C:79 , ARG C:81 , LEU C:94 , LEU C:103 , TYR C:106 , LYS C:125 , FE C:179 , DBH C:180 , DBH C:182 , HOH C:202
BINDING SITE FOR RESIDUE DBH C 181
16
BC7
SOFTWARE
TYR C:106 , LYS C:125 , LYS C:134 , FE C:179 , DBH C:180 , DBH C:181 , HOH C:183 , HOH C:197
BINDING SITE FOR RESIDUE DBH C 182
17
BC8
SOFTWARE
THR A:54 , TYR A:138
BINDING SITE FOR RESIDUE CL A 183
18
BC9
SOFTWARE
THR B:54 , TYR B:138
BINDING SITE FOR RESIDUE CL B 183
19
CC1
SOFTWARE
THR D:54 , TYR D:138
BINDING SITE FOR RESIDUE CL D 183
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: LIPOCALIN (A:21-34,B:21-34,C:21-34,D: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
4
A:21-34
B:21-34
C:21-34
D:21-34
[
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]
Exons
(6, 24)
Info
All Exons
Exon 1.2d (A:4-26 | B:3-26 | C:5-26 | D:5-26)
Exon 1.3 (A:27-72 | B:27-72 | C:27-72 | D:27...)
Exon 1.6b (A:72-99 | B:72-99 | C:72-99 | D:72...)
Exon 1.7 (A:99-139 | B:99-139 | C:99-139 | D...)
Exon 1.8 (A:139-173 | B:139-173 | C:139-173 ...)
Exon 1.9b (A:173-178 | B:173-177 | C:173-178 ...)
View:
Select:
Label:
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
4
A:4-26
B:3-26
C:5-26
D:5-26
23
24
22
22
1.3
ENST00000373017
3
ENSE00000984625
chr9:
130912517-130912653
137
NGAL_HUMAN
47-92
46
4
A:27-72
B:27-72
C:27-72
D:27-72
46
46
46
46
1.6b
ENST00000373017
6b
ENSE00000984626
chr9:
130913917-130913996
80
NGAL_HUMAN
92-119
28
4
A:72-99
B:72-99
C:72-99
D:72-99
28
28
28
28
1.7
ENST00000373017
7
ENSE00000984627
chr9:
130914185-130914304
120
NGAL_HUMAN
119-159
41
4
A:99-139
B:99-139
C:99-139
D:99-139
41
41
41
41
1.8
ENST00000373017
8
ENSE00001419823
chr9:
130914462-130914563
102
NGAL_HUMAN
159-193
35
4
A:139-173
B:139-173
C:139-173
D:139-173
35
35
35
35
1.9b
ENST00000373017
9b
ENSE00001459311
chr9:
130915379-130915412
34
NGAL_HUMAN
193-198
6
4
A:173-178
B:173-177
C:173-178
D:173-178
6
5
6
6
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3u0da_ (A:)
1b: SCOP_d3u0db_ (B:)
1c: SCOP_d3u0dc_ (C:)
1d: SCOP_d3u0dd_ (D:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d3u0da_
A:
1b
d3u0db_
B:
1c
d3u0dc_
C:
1d
d3u0dd_
D:
[
close SCOP info
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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 D
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