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4DJD
Asym. Unit
Info
Asym.Unit (663 KB)
Biol.Unit 1 (653 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FOLATE-FREE CORRINOID IRON-SULFUR PROTEIN (CFESP) IN COMPLEX WITH ITS METHYLTRANSFERASE (METR)
Authors
:
Y. Kung, T. I. Doukov, L. C. Blasiak, C. L. Drennan
Date
:
01 Feb 12 (Deposition) - 14 Mar 12 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.38
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Tim Barrel, Rossmann Fold, B12-Dependent Methyltransferase, Transferase-Vitamin-Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kung, N. Ando, T. I. Doukov, L. C. Blasiak, G. Bender, J. Seravalli, S. W. Ragsdale, C. L. Drennan
Visualizing Molecular Juggling Within A B12-Dependent Methyltransferase Complex.
Nature V. 484 265 2012
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
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)
3j: GLYCEROL (GOLj)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B12
2
Ligand/Ion
COBALAMIN
2
CA
2
Ligand/Ion
CALCIUM ION
3
GOL
10
Ligand/Ion
GLYCEROL
4
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:222 , ASP A:224 , HOH A:427 , HOH A:430 , HOH A:433
BINDING SITE FOR RESIDUE CA A 301
02
AC2
SOFTWARE
GLY B:222 , ASP B:224 , HOH B:422 , HOH B:430
BINDING SITE FOR RESIDUE CA B 301
03
AC3
SOFTWARE
PRO C:13 , ASN C:16 , CYS C:17 , GLY C:18 , CYS C:20 , CYS C:25 , PHE C:28 , CYS C:42 , PRO C:43
BINDING SITE FOR RESIDUE SF4 C 501
04
AC4
SOFTWARE
VAL B:168 , PRO C:318 , VAL C:339 , THR C:340 , PHE C:343 , LEU C:345 , THR C:346 , VAL C:350 , GLY C:370 , LEU C:371 , SER C:372 , VAL C:373 , LEU C:374 , THR C:375 , ALA C:378 , ASP C:379 , GLY C:429 , PRO C:430 , ARG C:431 , GLU C:432 , ALA C:433 , PRO D:188 , LEU D:189 , TYR D:226
BINDING SITE FOR RESIDUE B12 C 502
05
AC5
SOFTWARE
ASP D:38 , PRO D:42 , PHE D:43 , ILE D:50 , PRO D:54 , ARG D:235 , LEU D:292 , GLY D:295 , ALA D:296 , HIS D:297
BINDING SITE FOR RESIDUE GOL D 401
06
AC6
SOFTWARE
ASP D:115 , HOH D:562 , GLY F:94 , ALA F:95 , ASP F:96 , LYS F:311 , HOH F:583
BINDING SITE FOR RESIDUE GOL D 402
07
AC7
SOFTWARE
ASP D:115 , ARG F:53 , ASP F:96 , LYS F:311 , ASP F:315 , HOH F:559
BINDING SITE FOR RESIDUE GOL D 403
08
AC8
SOFTWARE
HIS D:45 , ILE D:50 , HOH D:507 , GLU E:199 , ASN E:200 , HOH E:663
BINDING SITE FOR RESIDUE GOL D 404
09
AC9
SOFTWARE
LYS D:122 , GLN D:126 , GLU D:157
BINDING SITE FOR RESIDUE GOL D 405
10
BC1
SOFTWARE
PRO E:13 , LYS E:15 , ASN E:16 , CYS E:17 , GLY E:18 , GLU E:19 , CYS E:20 , CYS E:25 , CYS E:42
BINDING SITE FOR RESIDUE SF4 E 501
11
BC2
SOFTWARE
VAL A:168 , ASN A:203 , PRO E:318 , TYR E:338 , VAL E:339 , THR E:340 , PHE E:343 , THR E:346 , SER E:349 , GLY E:370 , LEU E:371 , SER E:372 , VAL E:373 , LEU E:374 , THR E:375 , ALA E:378 , ASP E:379 , PRO E:408 , PRO E:430 , ARG E:431 , GLU E:432 , ALA E:433 , PRO F:188 , LEU F:189 , TYR F:226
BINDING SITE FOR RESIDUE B12 E 502
12
BC3
SOFTWARE
LYS D:170 , GLY E:210 , LEU E:211 , ASP E:244 , HOH E:614 , HOH E:655 , TYR F:323
BINDING SITE FOR RESIDUE GOL E 503
13
BC4
SOFTWARE
HIS D:144 , SER D:171 , HOH D:581 , ARG E:240
BINDING SITE FOR RESIDUE GOL E 504
14
BC5
SOFTWARE
ASP F:38 , PRO F:42 , PHE F:43 , ILE F:50 , PRO F:54 , ARG F:235 , LEU F:292 , GLY F:295 , ALA F:296 , HIS F:297
BINDING SITE FOR RESIDUE GOL F 401
15
BC6
SOFTWARE
GLU D:148 , ALA D:175 , HIS D:179 , HIS F:45 , ILE F:50 , MET F:318
BINDING SITE FOR RESIDUE GOL F 402
16
BC7
SOFTWARE
ASP F:8 , ARG F:9 , SER F:10 , GLN F:240
BINDING SITE FOR RESIDUE GOL F 403
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PTERIN_BINDING (A:1-246,B:1-246)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PTERIN_BINDING
PS50972
Pterin-binding domain profile.
ACSE_MOOTH
1-246
2
A:1-246
B:1-246
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Exons
(0, 0)
Info
All Exons
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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, 2)
Info
All SCOP Domains
1a: SCOP_d4djda_ (A:)
1b: SCOP_d4djdb_ (B:)
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Protein Domains
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(
)
Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Dihydropteroate synthetase-like
(59)
Family
:
Methyltetrahydrofolate-utiluzing methyltransferases
(16)
Protein domain
:
automated matches
(7)
Moorella thermoacetica [TaxId: 1525]
(4)
1a
d4djda_
A:
1b
d4djdb_
B:
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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
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Sorry, no Info available
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Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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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'
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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).
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Asym.Unit (663 KB)
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