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3FW5
Asym. Unit
Info
Asym.Unit (94 KB)
Biol.Unit 1 (34 KB)
Biol.Unit 2 (26 KB)
Biol.Unit 3 (35 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SIDEROCALIN (NGAL, LIPOCALIN 2) COMPLEXED WITH FERRIC 4-METHYL-CATECHOL
Authors
:
M. C. Clifton, R. K. Strong
Date
:
16 Jan 09 (Deposition) - 05 May 10 (Release) - 11 Aug 10 (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, 310-Helix, Glycoprotein, Pyrrolidone Carboxylic Acid, Secreted, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Bao, M. Clifton, T. M. Hoette, K. Mori, S. X. Deng, A. Qiu, M. Viltard, D. Williams, N. Paragas, T. Leete, R. Kulkarni, X. Li, B. Lee, A. Kalandadze, A. J. Ratner, J. C. Pizarro, K. M. Schmidt-Ott, D. W. Landry, K. N. Raymond, R. K. Strong, J. Barasch
Iron Traffics In Circulation Bound To A Siderocalin (Ngal)-Catechol Complex.
Nat. Chem. Biol. V. 6 602 2010
[
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Hetero Components
(5, 23)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
4a: 4-METHYLCATECHOL (MCTa)
4b: 4-METHYLCATECHOL (MCTb)
4c: 4-METHYLCATECHOL (MCTc)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
FE
3
Ligand/Ion
FE (III) ION
3
GOL
9
Ligand/Ion
GLYCEROL
4
MCT
3
Ligand/Ion
4-METHYLCATECHOL
5
NA
7
Ligand/Ion
SODIUM 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
TYR A:106 , MCT A:180
BINDING SITE FOR RESIDUE FE A 179
02
AC2
SOFTWARE
TYR A:106 , PHE A:123 , LYS A:125 , TYR A:132 , FE A:179 , HOH A:188
BINDING SITE FOR RESIDUE MCT A 180
03
AC3
SOFTWARE
LYS A:30 , TYR A:32 , ASP A:177
BINDING SITE FOR RESIDUE NA A 181
04
AC4
SOFTWARE
TRP A:79
BINDING SITE FOR RESIDUE CL A 184
05
AC5
SOFTWARE
ASN A:114 , HIS A:118 , HOH A:375 , ASN C:116
BINDING SITE FOR RESIDUE GOL A 185
06
AC6
SOFTWARE
PRO A:162 , ASN A:164 , HIS A:165 , HOH A:348 , LYS C:75
BINDING SITE FOR RESIDUE GOL A 186
07
AC7
SOFTWARE
GLN A:117 , HOH A:347 , ASN C:114
BINDING SITE FOR RESIDUE GOL A 187
08
AC8
SOFTWARE
MCT B:180
BINDING SITE FOR RESIDUE FE B 179
09
AC9
SOFTWARE
TYR B:106 , LYS B:125 , PHE B:133 , LYS B:134 , FE B:179
BINDING SITE FOR RESIDUE MCT B 180
10
BC1
SOFTWARE
LEU A:13 , HOH A:235 , GLN B:88 , HOH B:246
BINDING SITE FOR RESIDUE GOL B 181
11
BC2
SOFTWARE
MCT C:180
BINDING SITE FOR RESIDUE FE C 179
12
BC3
SOFTWARE
TYR C:106 , PHE C:123 , LYS C:125 , TYR C:132 , LYS C:134 , FE C:179 , GOL C:188 , HOH C:191
BINDING SITE FOR RESIDUE MCT C 180
13
BC4
SOFTWARE
SER C:112 , HIS C:118
BINDING SITE FOR RESIDUE NA C 181
14
BC5
SOFTWARE
LYS C:157 , HOH C:351
BINDING SITE FOR RESIDUE NA C 182
15
BC6
SOFTWARE
PHE C:22 , ASP C:24 , PRO C:85 , GLN C:88 , PRO C:89 , GLY C:90 , GLU C:91 , PHE C:92 , HOH C:205 , HOH C:240 , HOH C:242
BINDING SITE FOR RESIDUE GOL C 185
16
BC7
SOFTWARE
THR C:82 , GLY C:95 , ASN C:96 , TYR C:100
BINDING SITE FOR RESIDUE GOL C 186
17
BC8
SOFTWARE
THR C:93 , LEU C:94 , ILE C:97 , SER C:105 , TYR C:106 , HOH C:335
BINDING SITE FOR RESIDUE GOL C 187
18
BC9
SOFTWARE
LYS C:125 , TYR C:132 , MCT C:180
BINDING SITE FOR RESIDUE GOL C 188
19
CC1
SOFTWARE
LYS C:59 , GLU C:60 , ASP C:61
BINDING SITE FOR RESIDUE GOL C 189
[
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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, 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:4-26 | B:5-26 | C:4-26)
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 (gaps) | C:1...)
Exon 1.9b (A:173-178 | B:173-177 | C:173-177)
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
3
A:4-26
B:5-26
C:4-26
23
22
23
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 (gaps)
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_d3fw5a_ (A:)
1b: SCOP_d3fw5b_ (B:)
1c: SCOP_d3fw5c_ (C:)
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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
d3fw5a_
A:
1b
d3fw5b_
B:
1c
d3fw5c_
C:
[
close SCOP info
]
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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Label:
Sorry, no Info available
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
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