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2YIM
Biol. Unit 1
Info
Asym.Unit (276 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (138 KB)
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(1)
Title
:
THE ENOLISATION CHEMISTRY OF A THIOESTER-DEPENDENT RACEMASE: THE 1.4 A CRYSTAL STRUCTURE OF A COMPLEX WITH A PLANAR REACTION INTERMEDIATE ANALOGUE
Authors
:
S. Sharma, P. Bhaumik, R. Venkatesan, J. K. Hiltunen, E. Conzelmann, A. R. K. Wierenga
Date
:
16 May 11 (Deposition) - 28 Mar 12 (Release) - 04 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.41
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Isomerase, Methyl-Coa Racemase, Transition State, Molecular Dynamics, Qm/Mm, Oxyanion Hole
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Sharma, P. Bhaumik, W. Schmitz, R. Venkatesan, J. K. Hiltunen, E. Conzelmann, A. H. Juffer, R. K. Wierenga
The Enolization Chemistry Of A Thioester-Dependent Racemase: The 1. 4 A Crystal Structure Of A Reaction Intermediate Complex Characterized By Detailed Qm/Mm Calculations.
J Phys Chem B V. 116 3619 2012
(for further references see the
PDB file header
)
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
2a: 2-METHYLACETOACETYL COA (MC4a)
2b: 2-METHYLACETOACETYL COA (MC4b)
2c: 2-METHYLACETOACETYL COA (MC4c)
2d: 2-METHYLACETOACETYL COA (MC4d)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
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No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
MC4
2
Ligand/Ion
2-METHYLACETOACETYL COA
3
PO4
1
Ligand/Ion
PHOSPHATE ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC9 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:230 , HIS A:282 , ASP A:283 , HOH A:2406 , HOH A:2509
BINDING SITE FOR RESIDUE GOL A1361
2
AC2
SOFTWARE
ILE A:16 , ARG A:38 , ALA A:59 , ASP A:60 , LEU A:61 , LYS A:62 , GLY A:83 , TYR A:84 , ARG A:85 , VAL A:88 , ARG A:91 , LEU A:92 , GLY A:125 , HIS A:126 , ASP A:127 , TYR A:130 , ASP A:156 , HOH A:2025 , HOH A:2046 , HOH A:2110 , HOH A:2131 , HOH A:2140 , HOH A:2149 , HOH A:2151 , HOH A:2245 , HOH A:2510 , HOH A:2511 , HOH A:2512 , HOH A:2513 , HOH A:2514 , HOH A:2515 , HOH A:2516
BINDING SITE FOR RESIDUE MC4 A1363
3
AC3
SOFTWARE
HIS A:308 , ASN A:309 , ARG B:233 , HOH B:2258
BINDING SITE FOR RESIDUE PO4 B1361
4
AC4
SOFTWARE
THR A:209 , ASP A:210 , THR A:211 , THR B:209 , ASP B:210 , HOH B:2223 , HOH B:2235
BINDING SITE FOR RESIDUE GOL B1362
5
AC5
SOFTWARE
TYR A:224 , HOH A:2352 , HOH A:2353 , ARG B:38 , ALA B:59 , ASP B:60 , LEU B:61 , LYS B:62 , GLY B:83 , TYR B:84 , ARG B:85 , VAL B:88 , ARG B:91 , LEU B:92 , GLY B:125 , HIS B:126 , ASP B:127 , TYR B:130 , ASP B:156 , HOH B:2023 , HOH B:2038 , HOH B:2089 , HOH B:2090 , HOH B:2104 , HOH B:2111 , HOH B:2120 , HOH B:2122 , HOH B:2191 , HOH B:2394 , HOH B:2395 , HOH B:2396 , HOH B:2397 , HOH B:2398
BINDING SITE FOR RESIDUE MC4 B1363
6
AC9
SOFTWARE
HIS A:282 , HOH A:2362 , HOH A:2408 , HOH A:2417 , HOH A:2418 , HIS D:282 , HOH D:2330 , HOH D:2333 , HOH D:2418
BINDING SITE FOR RESIDUE PO4 D1361
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2yima_ (A:)
1b: SCOP_d2yimb_ (B:)
1c: SCOP_d2yimd_ (D:)
2a: SCOP_d2yimc_ (C:)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
CoA-transferase family III (CaiB/BaiF)
(35)
Superfamily
:
CoA-transferase family III (CaiB/BaiF)
(35)
Family
:
CoA-transferase family III (CaiB/BaiF)
(35)
Protein domain
:
2-methylacyl-CoA racemase Mcr
(7)
Mycobacterium tuberculosis [TaxId: 1773]
(7)
1a
d2yima_
A:
1b
d2yimb_
B:
1c
d2yimd_
D:
Protein domain
:
automated matches
(9)
Mycobacterium tuberculosis [TaxId: 83332]
(1)
2a
d2yimc_
C:
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CATH Domains
(0, 0)
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Pfam Domains
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (276 KB)
Header - Asym.Unit
Biol.Unit 1 (138 KB)
Header - Biol.Unit 1
Biol.Unit 2 (138 KB)
Header - Biol.Unit 2
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