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2GUF
Asym. Unit
Info
Asym.Unit (111 KB)
Biol.Unit 1 (103 KB)
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(1)
Title
:
IN MESO CRYSTAL STRUCTURE OF THE COBALAMIN TRANSPORTER, BTUB
Authors
:
M. Caffrey, V. Cherezov, E. Yamashita, W. A. Cramer
Date
:
29 Apr 06 (Deposition) - 05 Dec 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Beta Barrel, Cubic Mesophase, Cobalamin, Btub, Colicin, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Cherezov, E. Yamashita, W. Liu, M. Zhalnina, W. A. Cramer, M. Caffre
In Meso Structure Of The Cobalamin Transporter, Btub, At 1. 95 A Resolution.
J. Mol. Biol. V. 364 716 2006
[
close entry info
]
Hetero Components
(3, 16)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
3a: 1-MONOOLEOYL-RAC-GLYCEROL (MPGa)
3b: 1-MONOOLEOYL-RAC-GLYCEROL (MPGb)
3c: 1-MONOOLEOYL-RAC-GLYCEROL (MPGc)
3d: 1-MONOOLEOYL-RAC-GLYCEROL (MPGd)
3e: 1-MONOOLEOYL-RAC-GLYCEROL (MPGe)
3f: 1-MONOOLEOYL-RAC-GLYCEROL (MPGf)
3g: 1-MONOOLEOYL-RAC-GLYCEROL (MPGg)
3h: 1-MONOOLEOYL-RAC-GLYCEROL (MPGh)
3i: 1-MONOOLEOYL-RAC-GLYCEROL (MPGi)
3j: 1-MONOOLEOYL-RAC-GLYCEROL (MPGj)
3k: 1-MONOOLEOYL-RAC-GLYCEROL (MPGk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
1
Ligand/Ion
FORMIC ACID
2
MPD
4
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
MPG
11
Ligand/Ion
1-MONOOLEOYL-RAC-GLYCEROL
[
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]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:214 , TYR A:256 , ASN A:302 , LEU A:342 , ALA A:466 , VAL A:479 , TYR A:481 , MPG A:704 , MPG A:705
BINDING SITE FOR RESIDUE MPG A 701
02
AC2
SOFTWARE
ILE A:140 , SER A:141 , ALA A:142 , VAL A:154 , ASP A:171 , LYS A:200 , THR A:201 , LEU A:202 , GLY A:222 , ASP A:224 , LEU A:559 , GLY A:590 , TYR A:592
BINDING SITE FOR RESIDUE MPG A 702
03
AC3
SOFTWARE
LEU A:254 , SER A:263 , VAL A:298 , TRP A:300 , VAL A:315 , THR A:338 , TYR A:383 , HOH A:1143 , HOH A:1153
BINDING SITE FOR RESIDUE MPG A 703
04
AC4
SOFTWARE
ASN A:302 , ALA A:313 , GLY A:314 , ALA A:357 , ARG A:358 , GLY A:369 , THR A:370 , TRP A:371 , THR A:391 , TRP A:431 , ALA A:468 , PHE A:470 , THR A:472 , MPG A:701 , MPG A:705 , MPD A:904
BINDING SITE FOR RESIDUE MPG A 704
05
AC5
SOFTWARE
ILE A:311 , GLY A:344 , ALA A:357 , TRP A:371 , THR A:472 , HIS A:477 , VAL A:479 , VAL A:503 , TYR A:505 , MPG A:701 , MPG A:704
BINDING SITE FOR RESIDUE MPG A 705
06
AC6
SOFTWARE
TYR A:296 , TRP A:317 , LYS A:319
BINDING SITE FOR RESIDUE MPG A 706
07
AC7
SOFTWARE
GLY A:307 , GLN A:346 , TYR A:520 , TYR A:522 , SER A:545 , MPG A:711 , HOH A:1133 , HOH A:1156
BINDING SITE FOR RESIDUE MPG A 707
08
AC8
SOFTWARE
THR A:138 , VAL A:154 , TYR A:221 , GLN A:248 , PHE A:594 , HOH A:1103
BINDING SITE FOR RESIDUE MPG A 708
09
AC9
SOFTWARE
LEU A:160 , GLY A:161 , ASP A:162 , LYS A:163 , THR A:164 , HIS A:208 , GLY A:216 , PHE A:217 , TYR A:586
BINDING SITE FOR RESIDUE MPG A 709
10
BC1
SOFTWARE
THR A:373 , SER A:374 , ALA A:375 , ALA A:387 , SER A:388 , GLU A:419 , GLY A:420 , ALA A:421 , MPG A:711
BINDING SITE FOR RESIDUE MPG A 710
11
BC2
SOFTWARE
GLN A:346 , THR A:373 , TYR A:389 , LYS A:416 , TRP A:418 , MPG A:707 , MPG A:710
BINDING SITE FOR RESIDUE MPG A 711
12
BC3
SOFTWARE
THR A:30 , ARG A:31 , GLN A:105 , ARG A:106 , HOH A:1162
BINDING SITE FOR RESIDUE FMT A 801
13
BC4
SOFTWARE
ASN A:86 , ASP A:95 , TYR A:223 , SER A:272 , MET A:293 , HOH A:999 , HOH A:1051
BINDING SITE FOR RESIDUE MPD A 901
14
BC5
SOFTWARE
GLN A:318 , GLN A:320 , GLN A:335 , ASN A:337 , ALA A:395 , ASN A:397 , HOH A:1167
BINDING SITE FOR RESIDUE MPD A 902
15
BC6
SOFTWARE
SER A:91 , ALA A:94 , TYR A:405 , TYR A:446 , TYR A:453 , HOH A:1026
BINDING SITE FOR RESIDUE MPD A 903
16
BC7
SOFTWARE
SER A:286 , SER A:359 , HIS A:368 , GLY A:369 , ALA A:427 , ASP A:471 , MPG A:704
BINDING SITE FOR RESIDUE MPD A 904
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: TONB_DEPENDENT_REC_2 (A:582-594)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TONB_DEPENDENT_REC_2
PS01156
TonB-dependent receptor proteins signature 2.
BTUB_ECOLI
597-614
1
A:582-594
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2gufa_ (A:)
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(
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(
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Folds
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(
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Superfamilies
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(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Transmembrane beta-barrels
(143)
Superfamily
:
Porins
(99)
Family
:
Ligand-gated protein channel
(29)
Protein domain
:
Outer membrane cobalamin transporter BtuB
(12)
Escherichia coli [TaxId: 562]
(12)
1a
d2gufa_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2gufA02 (A:131-594)
2a: CATH_2gufA01 (A:7-130)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Maltoporin; Chain A
(39)
Homologous Superfamily
:
[code=2.40.170.20, no name defined]
(28)
Escherichia coli. Organism_taxid: 562.
(3)
1a
2gufA02
A:131-594
Architecture
:
Beta Complex
(381)
Topology
:
Ferric Hydroxamate Uptake Protein; Chain A, domain 1
(37)
Homologous Superfamily
:
Ferric Hydroxamate Uptake Protein; Chain A, domain 1
(36)
Escherichia coli. Organism_taxid: 562.
(3)
2a
2gufA01
A:7-130
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Protein
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Sidechain
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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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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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (111 KB)
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