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1VR5
Biol. Unit 1
Info
Asym.Unit (214 KB)
Biol.Unit 1 (106 KB)
Biol.Unit 2 (104 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF OLIGOPEPTIDE ABC TRANSPORTER, PERIPLASMIC OLIGOPEPTIDE-BINDING (TM1223) FROM THERMOTOGA MARITIMA AT 1.73 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
11 Feb 05 (Deposition) - 08 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.73
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Tm1223, Oligopeptide Abc Transporter, Periplasmic Oligopeptide- Binding, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Oligopeptide Abc Transporter, Periplasmic Oligopeptide-Binding (Tm1223) From Thermotoga Maritima At 1. 73 A Resolution
To Be Published
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Hetero Components
(5, 31)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
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: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
5a: FORMIC ACID (FMTa)
5b: FORMIC ACID (FMTb)
6a: SELENOMETHIONINE (MSEa)
6b: SELENOMETHIONINE (MSEb)
6c: SELENOMETHIONINE (MSEc)
6d: SELENOMETHIONINE (MSEd)
6e: SELENOMETHIONINE (MSEe)
6f: SELENOMETHIONINE (MSEf)
6g: SELENOMETHIONINE (MSEg)
6h: SELENOMETHIONINE (MSEh)
6i: SELENOMETHIONINE (MSEi)
6j: SELENOMETHIONINE (MSEj)
6k: SELENOMETHIONINE (MSEk)
6l: SELENOMETHIONINE (MSEl)
6m: SELENOMETHIONINE (MSEm)
6n: SELENOMETHIONINE (MSEn)
6o: SELENOMETHIONINE (MSEo)
6p: SELENOMETHIONINE (MSEp)
6q: SELENOMETHIONINE (MSEq)
6r: SELENOMETHIONINE (MSEr)
7a: SODIUM ION (NAa)
7b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
16
Ligand/Ion
1,2-ETHANEDIOL
4
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5
FMT
2
Ligand/Ion
FORMIC ACID
6
MSE
9
Mod. Amino Acid
SELENOMETHIONINE
7
NA
-1
Ligand/Ion
SODIUM ION
[
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Sites
(22, 22)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC9 (SOFTWARE)
15: DC2 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC5 (SOFTWARE)
18: DC6 (SOFTWARE)
19: DC7 (SOFTWARE)
20: DC8 (SOFTWARE)
21: EC1 (SOFTWARE)
22: EC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:362 , ASP A:366 , PHE A:368 , GLU A:370
BINDING SITE FOR RESIDUE NA A 1
02
AC3
SOFTWARE
ASN A:128 , ARG A:149 , HOH A:1149
BINDING SITE FOR RESIDUE CL A 3
03
AC5
SOFTWARE
VAL A:263 , GLU A:520 , ASN A:525 , TRP A:526 , HOH A:847
BINDING SITE FOR RESIDUE ACT A 6
04
AC6
SOFTWARE
LYS A:257 , VAL A:263 , THR A:264 , GLU A:267
BINDING SITE FOR RESIDUE ACT A 7
05
AC8
SOFTWARE
PRO A:46 , TRP A:47 , ALA A:49 , ALA A:51 , HOH A:579 , HOH A:606
BINDING SITE FOR RESIDUE ACT A 9
06
AC9
SOFTWARE
TYR A:385 , LYS A:411 , TYR A:412 , PRO A:413 , ASP A:414
BINDING SITE FOR RESIDUE EPE A 5
07
BC3
SOFTWARE
EDO A:19 , TRP A:81 , SER A:83 , ASN A:84 , TYR A:150 , ASN A:484 , HOH A:904 , HOH A:1120
BINDING SITE FOR RESIDUE EDO A 12
08
BC4
SOFTWARE
EDO A:14 , GLY A:437 , VAL A:438 , TRP A:542 , HOH A:790
BINDING SITE FOR RESIDUE EDO A 13
09
BC5
SOFTWARE
EDO A:13 , GLN A:155 , THR A:435 , HOH A:629 , HOH A:701
BINDING SITE FOR RESIDUE EDO A 14
10
BC6
SOFTWARE
GLN A:98 , ASP A:99 , GLY A:100 , GLU A:182 , ASN A:207 , HOH A:617 , HOH A:620 , HOH A:923
BINDING SITE FOR RESIDUE EDO A 15
11
BC7
SOFTWARE
PHE A:62 , GLY A:79 , TYR A:87 , LEU A:157 , HOH A:650 , HOH A:818 , HOH A:1022
BINDING SITE FOR RESIDUE EDO A 16
12
CC1
SOFTWARE
EDO A:12 , ASN A:484 , ASP A:485
BINDING SITE FOR RESIDUE EDO A 19
13
CC5
SOFTWARE
PHE A:110 , HOH A:649
BINDING SITE FOR RESIDUE EDO A 558
14
CC9
SOFTWARE
VAL A:338 , TYR A:342 , GLU A:498
BINDING SITE FOR RESIDUE EDO A 559
15
DC2
SOFTWARE
ARG A:24 , TYR A:29 , GLU A:242 , HOH A:1042 , HOH A:1044 , HOH A:1054
BINDING SITE FOR RESIDUE EDO A 560
16
DC4
SOFTWARE
TRP A:35 , VAL A:228 , LEU A:229 , SER A:230 , ASN A:231 , PHE A:248
BINDING SITE FOR RESIDUE EDO A 562
17
DC5
SOFTWARE
PRO A:125 , VAL A:126 , TRP A:129 , GLU A:152 , MSE A:156 , HOH A:1149 , HOH A:1150
BINDING SITE FOR RESIDUE EDO A 564
18
DC6
SOFTWARE
THR A:388 , MSE A:391 , GLN A:395 , HOH A:954
BINDING SITE FOR RESIDUE EDO A 565
19
DC7
SOFTWARE
GLU A:472 , LYS A:495 , ILE A:499
BINDING SITE FOR RESIDUE EDO A 566
20
DC8
SOFTWARE
SER A:194 , TRP A:195 , HOH A:813 , HOH A:1052
BINDING SITE FOR RESIDUE EDO A 567
21
EC1
SOFTWARE
SER A:290 , PRO A:292 , ARG A:295 , HOH A:922
BINDING SITE FOR RESIDUE FMT A 568
22
EC2
SOFTWARE
ASP A:503
BINDING SITE FOR RESIDUE FMT A 569
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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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End label:
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1vr5a1 (A:23-557)
1b: SCOP_d1vr5b_ (B:)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Oligo-peptide binding protein (OPPA)
(34)
Thermotoga maritima [TaxId: 2336]
(1)
1a
d1vr5a1
A:23-557
1b
d1vr5b_
B:
[
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CATH Domains
(0, 0)
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all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_SBP_bac_5_1vr5B01 (B:70-454)
1b: PFAM_SBP_bac_5_1vr5B02 (B:70-454)
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Clan
:
PBP
(391)
Family
:
SBP_bac_5
(33)
Thermotoga maritima
(2)
1a
SBP_bac_5-1vr5B01
B:70-454
1b
SBP_bac_5-1vr5B02
B:70-454
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