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4O9S
Biol. Unit 3
Info
Asym.Unit (72 KB)
Biol.Unit 1 (35 KB)
Biol.Unit 2 (35 KB)
Biol.Unit 3 (66 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RETINOL-BINDING PROTEIN 4 (RBP4)IN COMPLEX WITH A NON-RETINOID LIGAND
Authors
:
Z. Wang, S. Johnstone, N. P. Walker
Date
:
02 Jan 14 (Deposition) - 02 Jul 14 (Release) - 02 Jul 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Retinol Binding, Disease Mutation, Retinol-Binding, Secreted, Sensory Transduction, Transport, Vision, Vitamin A, Transport Protein, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Wang, R. Connors, P. Fan, X. Wang, Z. Wang, J. Liu, F. Kayser, J. C. Medina, S. Johnstone, H. Xu, S. Thibault, N. Walker, M. Conn, Y. Zhang, Q. Liu, M. P. Grillo, A. Motani, P. Coward, Z. Wang
Structure-Assisted Discovery Of The First Non-Retinoid Ligands For Retinol-Binding Protein 4.
Bioorg. Med. Chem. Lett. V. 24 2885 2014
[
close entry info
]
Hetero Components
(3, 15)
Info
All Hetero Components
1a: 1-[4-(8LAMBDA~4~-CYCLOPENTA[4,5]TH... (2RYa)
1b: 1-[4-(8LAMBDA~4~-CYCLOPENTA[4,5]TH... (2RYb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2RY
1
Ligand/Ion
1-[4-(8LAMBDA~4~-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-YL)PIPERAZIN-1-YL]-2-[2-(TRIFLUOROMETHYL)PHENYL]ETHANONE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
13
Ligand/Ion
1,2-ETHANEDIOL
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
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Sites
(31, 31)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:35 , PHE A:36 , LEU A:37 , ALA A:55 , ALA A:57 , MET A:73 , VAL A:74 , GLY A:75 , MET A:88 , TYR A:90 , ASP A:102 , ARG A:121 , TYR A:133 , PHE A:135 , HOH A:303
BINDING SITE FOR RESIDUE 2RY A 201
02
AC2
SOFTWARE
GLU A:81 , ASP A:82
BINDING SITE FOR RESIDUE EDO A 202
03
AC3
SOFTWARE
PHE A:9 , ARG A:10 , VAL A:107 , ARG A:155 , GLU A:158 , EDO A:211
BINDING SITE FOR RESIDUE EDO A 203
04
AC4
SOFTWARE
ASP A:126 , LEU A:144 , HOH A:311
BINDING SITE FOR RESIDUE EDO A 204
05
AC5
SOFTWARE
THR A:80 , GLU A:81
BINDING SITE FOR RESIDUE EDO A 205
06
AC6
SOFTWARE
GLN A:156 , ARG A:163 , TYR A:165
BINDING SITE FOR RESIDUE EDO A 206
07
AC7
SOFTWARE
VAL A:42 , THR A:56 , ALA A:57 , LYS A:58
BINDING SITE FOR RESIDUE EDO A 207
08
AC8
SOFTWARE
ASP A:31 , GLN A:164 , ARG A:166
BINDING SITE FOR RESIDUE EDO A 208
09
AC9
SOFTWARE
LYS A:30 , ASP A:31 , PRO A:32 , GLU A:33 , ALA A:130 , ASP A:131 , SER A:132
BINDING SITE FOR RESIDUE EDO A 209
10
BC1
SOFTWARE
VAL A:42 , HIS A:170 , ASN A:171 , GLY A:172
BINDING SITE FOR RESIDUE EDO A 210
11
BC2
SOFTWARE
ARG A:10 , VAL A:11 , VAL A:107 , ARG A:155 , EDO A:203 , HOH A:313
BINDING SITE FOR RESIDUE EDO A 211
12
BC3
SOFTWARE
ASN A:142 , HIS A:170 , PEG A:217 , HOH A:354
BINDING SITE FOR RESIDUE EDO A 212
13
BC4
SOFTWARE
ASN A:66 , TRP A:67 , LEU B:35 , 2RY B:201
BINDING SITE FOR RESIDUE EDO A 213
14
BC5
SOFTWARE
TRP A:91 , TRP B:91 , EDO B:209 , HOH B:398
BINDING SITE FOR RESIDUE EDO A 214
15
BC6
SOFTWARE
ASP A:72 , ALA A:94 , SER A:95 , PHE A:96
BINDING SITE FOR RESIDUE CL A 215
16
BC7
SOFTWARE
TRP B:67
BINDING SITE FOR RESIDUE CL A 216
17
BC8
SOFTWARE
ASP A:103 , CYS A:120 , HIS A:170 , ASN A:171 , EDO A:212 , HOH A:400
BINDING SITE FOR RESIDUE PEG A 217
18
BC9
SOFTWARE
EDO A:213 , LEU B:35 , PHE B:36 , LEU B:37 , ALA B:55 , ALA B:57 , VAL B:61 , MET B:73 , VAL B:74 , GLY B:75 , MET B:88 , TYR B:90 , ASP B:102 , ARG B:121 , TYR B:133 , PHE B:135 , HOH B:307
BINDING SITE FOR RESIDUE 2RY B 201
19
CC1
SOFTWARE
GLU A:13 , ASN A:14 , PRO B:145 , GLU B:147
BINDING SITE FOR RESIDUE EDO B 202
20
CC2
SOFTWARE
PHE B:9 , ARG B:10 , VAL B:107 , ARG B:155 , GLU B:158
BINDING SITE FOR RESIDUE EDO B 203
21
CC3
SOFTWARE
ASP B:3
BINDING SITE FOR RESIDUE EDO B 204
22
CC4
SOFTWARE
ARG B:10 , VAL B:11 , LYS B:12 , VAL B:107 , ASP B:108 , ARG B:155 , HOH B:318
BINDING SITE FOR RESIDUE EDO B 205
23
CC5
SOFTWARE
ASP B:103 , CYS B:120 , LEU B:123 , VAL B:169 , HIS B:170 , EDO B:210 , EDO B:214
BINDING SITE FOR RESIDUE EDO B 206
24
CC6
SOFTWARE
LYS B:30 , ASP B:31 , GLN B:164 , HOH B:394
BINDING SITE FOR RESIDUE EDO B 207
25
CC7
SOFTWARE
LYS B:87 , ASN B:101 , ASP B:102 , ASP B:103 , ASN B:171 , EDO B:213 , EDO B:214
BINDING SITE FOR RESIDUE EDO B 208
26
CC8
SOFTWARE
LEU A:97 , EDO A:214 , TRP B:91 , GLY B:92 , LEU B:97 , GLN B:98 , HOH B:341
BINDING SITE FOR RESIDUE EDO B 209
27
CC9
SOFTWARE
LEU B:123 , PRO B:141 , ASN B:142 , HIS B:170 , EDO B:206 , EDO B:214 , HOH B:368 , HOH B:411
BINDING SITE FOR RESIDUE EDO B 210
28
DC1
SOFTWARE
ARG B:153 , GLN B:156 , ARG B:163 , GLN B:164 , TYR B:165 , HOH B:326
BINDING SITE FOR RESIDUE EDO B 212
29
DC2
SOFTWARE
ASN B:101 , ASP B:102 , ARG B:121 , VAL B:169 , ASN B:171 , EDO B:208 , HOH B:343
BINDING SITE FOR RESIDUE EDO B 213
30
DC3
SOFTWARE
LYS B:87 , ASP B:103 , HIS B:170 , ASN B:171 , EDO B:206 , EDO B:208 , EDO B:210
BINDING SITE FOR RESIDUE EDO B 214
31
DC4
SOFTWARE
ASP B:72 , ALA B:94 , SER B:95 , PHE B:96
BINDING SITE FOR RESIDUE CL B 215
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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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
all PFAM domains
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Sorry, no Info available
[
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Atom Selection
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)
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Protein & NOT Site
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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