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5REQ
Asym. Unit
Info
Asym.Unit (457 KB)
Biol.Unit 1 (227 KB)
Biol.Unit 2 (228 KB)
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(1)
Title
:
METHYLMALONYL-COA MUTASE, Y89F MUTANT, SUBSTRATE COMPLEX
Authors
:
P. R. Evans, N. H. Thomae
Date
:
03 Aug 98 (Deposition) - 12 Aug 98 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Isomerase, Mutase, Intramolecular Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. H. Thoma, T. W. Meier, P. R. Evans, P. F. Leadlay
Stabilization Of Radical Intermediates By An Active-Site Tyrosine Residue In Methylmalonyl-Coa Mutase.
Biochemistry V. 37 14386 1998
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
3a: METHYLMALONYL(CARBADETHIA)-COENZYM... (MCDa)
3b: METHYLMALONYL(CARBADETHIA)-COENZYM... (MCDb)
4a: SUCCINYL(CARBADETHIA)-COENZYME A (SCDa)
4b: SUCCINYL(CARBADETHIA)-COENZYME A (SCDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B12
2
Ligand/Ion
COBALAMIN
2
GOL
4
Ligand/Ion
GLYCEROL
3
MCD
2
Ligand/Ion
METHYLMALONYL(CARBADETHIA)-COENZYME A
4
SCD
2
Ligand/Ion
SUCCINYL(CARBADETHIA)-COENZYME A
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:117 , LEU A:119 , HIS A:122 , ALA A:139 , VAL A:206 , ARG A:207 , THR A:209 , HIS A:244 , GLU A:247 , GLY A:333 , TRP A:334 , GLU A:370 , ALA A:371 , ALA A:373 , LEU A:374 , GLN A:454 , LEU A:602 , GLY A:609 , HIS A:610 , ASP A:611 , ARG A:612 , GLY A:613 , VAL A:616 , ILE A:617 , TYR A:621 , SER A:655 , LEU A:657 , GLY A:659 , GLY A:685 , GLY A:686 , VAL A:687 , TYR A:705 , THR A:706 , THR A:709 , SCD A:1801 , MCD A:1802 , HOH A:5096 , HOH A:5103 , HOH A:5108 , HOH A:5144 , HOH A:5174 , HOH A:5205 , HOH A:5280 , HOH A:5406 , HOH A:5417 , HOH A:5443 , HOH A:5452
BINDING SITE FOR RESIDUE B12 A 1800
02
AC2
SOFTWARE
TYR A:75 , THR A:77 , MET A:78 , ARG A:82 , THR A:85 , ARG A:87 , PHE A:89 , SER A:114 , SER A:162 , SER A:164 , THR A:166 , THR A:195 , GLN A:197 , ARG A:207 , ASN A:236 , TYR A:243 , HIS A:244 , ARG A:283 , SER A:285 , PHE A:287 , ARG A:326 , HIS A:328 , GLN A:330 , GLN A:361 , SER A:362 , B12 A:1800 , HOH A:5005 , HOH A:5006 , HOH A:5024 , HOH A:5033 , HOH A:5034 , HOH A:5035 , HOH A:5066 , HOH A:5099 , HOH A:5107 , HOH A:5119 , HOH A:5193 , HOH A:5244 , HOH A:5490 , ARG B:45
BINDING SITE FOR RESIDUE SCD A 1801
03
AC3
SOFTWARE
TYR A:75 , THR A:77 , MET A:78 , ARG A:82 , THR A:85 , ARG A:87 , PHE A:89 , SER A:114 , SER A:164 , THR A:166 , THR A:195 , GLN A:197 , ARG A:207 , ASN A:236 , TYR A:243 , HIS A:244 , ARG A:283 , SER A:285 , PHE A:287 , THR A:327 , HIS A:328 , GLN A:330 , GLN A:361 , SER A:362 , B12 A:1800 , HOH A:5005 , HOH A:5006 , HOH A:5024 , HOH A:5033 , HOH A:5034 , HOH A:5035 , HOH A:5066 , HOH A:5099 , HOH A:5107 , HOH A:5119 , HOH A:5193 , HOH A:5244 , HOH A:5490 , ARG B:45
BINDING SITE FOR RESIDUE MCD A 1802
04
AC4
SOFTWARE
PHE C:117 , LEU C:119 , HIS C:122 , ALA C:139 , VAL C:206 , ARG C:207 , THR C:209 , TYR C:243 , HIS C:244 , GLU C:247 , GLY C:333 , TRP C:334 , LEU C:336 , GLU C:370 , ALA C:371 , ALA C:373 , LEU C:374 , GLN C:454 , LEU C:602 , ASP C:608 , GLY C:609 , HIS C:610 , ASP C:611 , ARG C:612 , GLY C:613 , ILE C:617 , TYR C:621 , SER C:655 , LEU C:657 , ALA C:658 , GLY C:659 , GLY C:685 , GLY C:686 , VAL C:687 , TYR C:705 , THR C:706 , THR C:709 , SER C:714 , SCD C:2801 , MCD C:2802 , HOH C:4096 , HOH C:4103 , HOH C:4108 , HOH C:4144 , HOH C:4174 , HOH C:4205 , HOH C:4280 , HOH C:4406 , HOH C:4417 , HOH C:4443 , HOH C:4452
BINDING SITE FOR RESIDUE B12 C 2800
05
AC5
SOFTWARE
TYR C:75 , THR C:77 , MET C:78 , ARG C:82 , THR C:85 , ARG C:87 , PHE C:89 , SER C:114 , SER C:164 , THR C:166 , THR C:195 , GLN C:197 , ARG C:207 , ASN C:236 , TYR C:243 , HIS C:244 , ARG C:283 , SER C:285 , PHE C:287 , ARG C:326 , HIS C:328 , GLN C:330 , GLN C:361 , SER C:362 , B12 C:2800 , HOH C:4005 , HOH C:4006 , HOH C:4024 , HOH C:4033 , HOH C:4034 , HOH C:4035 , HOH C:4039 , HOH C:4066 , HOH C:4099 , HOH C:4107 , HOH C:4119 , HOH C:4193 , HOH C:4244 , HOH C:4490 , ARG D:45
BINDING SITE FOR RESIDUE SCD C 2801
06
AC6
SOFTWARE
TYR C:75 , THR C:77 , MET C:78 , ARG C:82 , THR C:85 , ARG C:87 , PHE C:89 , SER C:114 , SER C:164 , THR C:166 , THR C:195 , GLN C:197 , ARG C:207 , ASN C:236 , TYR C:243 , HIS C:244 , ARG C:283 , SER C:285 , PHE C:287 , HIS C:328 , GLN C:330 , GLN C:361 , SER C:362 , B12 C:2800 , HOH C:4005 , HOH C:4006 , HOH C:4024 , HOH C:4033 , HOH C:4034 , HOH C:4035 , HOH C:4039 , HOH C:4066 , HOH C:4099 , HOH C:4107 , HOH C:4119 , HOH C:4193 , HOH C:4244 , HOH C:4490 , ARG D:45
BINDING SITE FOR RESIDUE MCD C 2802
07
AC7
SOFTWARE
GLU B:177 , VAL B:216 , ASP B:219 , ARG B:223
BINDING SITE FOR RESIDUE GOL B 3001
08
AC8
SOFTWARE
THR B:98 , ARG B:100 , ALA B:106 , TRP B:107 , GLY B:354 , ALA B:355 , GLU B:356
BINDING SITE FOR RESIDUE GOL B 3002
09
AC9
SOFTWARE
GLU D:177 , VAL D:216 , TRP D:220 , ARG D:223
BINDING SITE FOR RESIDUE GOL D 3003
10
BC1
SOFTWARE
THR D:98 , ARG D:100 , ALA D:106 , TRP D:107 , GLY D:354 , ALA D:355
BINDING SITE FOR RESIDUE GOL D 3004
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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[
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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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d5reqa2 (A:561-728)
1b: SCOP_d5reqc2 (C:561-728)
2a: SCOP_d5reqb2 (B:476-638)
2b: SCOP_d5reqd2 (D:476-638)
3a: SCOP_d5reqa1 (A:4-560)
3b: SCOP_d5reqc1 (C:4-560)
4a: SCOP_d5reqb1 (B:20-475)
4b: SCOP_d5reqd1 (D:20-475)
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)
(
)
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)
(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Cobalamin (vitamin B12)-binding domain
(29)
Family
:
Cobalamin (vitamin B12)-binding domain
(29)
Protein domain
:
Methylmalonyl-CoA mutase alpha subunit, C-terminal domain
(8)
Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]
(8)
1a
d5reqa2
A:561-728
1b
d5reqc2
C:561-728
Protein domain
:
Methylmalonyl-CoA mutase beta subunit, C-terminal domain
(8)
Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]
(8)
2a
d5reqb2
B:476-638
2b
d5reqd2
D:476-638
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Cobalamin (vitamin B12)-dependent enzymes
(30)
Family
:
Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain
(16)
Protein domain
:
Methylmalonyl-CoA mutase alpha subunit, domain 1
(8)
Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]
(8)
3a
d5reqa1
A:4-560
3b
d5reqc1
C:4-560
Protein domain
:
Methylmalonyl-CoA mutase beta subunit, domain 1
(8)
Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]
(8)
4a
d5reqb1
B:20-475
4b
d5reqd1
D:20-475
[
close SCOP info
]
CATH Domains
(3, 10)
Info
all CATH domains
1a: CATH_5reqB02 (B:500-638)
1b: CATH_5reqA02 (A:563-726)
1c: CATH_5reqC02 (C:563-726)
1d: CATH_5reqD02 (D:500-638)
2a: CATH_5reqB01 (B:63-499)
2b: CATH_5reqA01 (A:38-559)
2c: CATH_5reqC01 (C:38-559)
2d: CATH_5reqD01 (D:63-499)
3a: CATH_5reqB03 (B:20-62)
3b: CATH_5reqD03 (D:20-62)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.280, no name defined]
(23)
Shermanii (Propionibacterium freudenreichii subsp)
(7)
1a
5reqB02
B:500-638
1b
5reqA02
A:563-726
1c
5reqC02
C:563-726
1d
5reqD02
D:500-638
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.240, no name defined]
(12)
Shermanii (Propionibacterium freudenreichii subsp)
(7)
2a
5reqB01
B:63-499
2b
5reqA01
A:38-559
2c
5reqC01
C:38-559
2d
5reqD01
D:63-499
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Regulator of G-protein Signalling 4; domain 1
(15)
Homologous Superfamily
:
[code=1.10.196.20, no name defined]
(1)
Shermanii (Propionibacterium freudenreichii subsp)
(1)
3a
5reqB03
B:20-62
3b
5reqD03
D:20-62
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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