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5M1D
Asym. Unit
Info
Asym.Unit (474 KB)
Biol.Unit 1 (925 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF N-TERMINALLY TAGGED UBID FROM E. COLI RECONSTITUTED WITH PRFMN COFACTOR
Authors
:
S. A. Marshall, D. Leys
Date
:
07 Oct 16 (Deposition) - 11 Jan 17 (Release) - 29 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Ubid, Decarboxylase, Ubiquinone Biosynthesis, Prfmn Binding, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. A. Marshall, K. Fisher, A. Ni Cheallaigh, M. D. White, K. A. Payne, D. A. Parker, S. E. Rigby, D. Leys
Oxidative Maturation And Structural Characterization Of Prenylated Fmn Binding By Ubid, A Decarboxylase Involved In Bacterial Ubiquinone Biosynthesis.
J. Biol. Chem. V. 292 4623 2017
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: 1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-T... (4LUa)
1b: 1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-T... (4LUb)
1c: 1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-T... (4LUc)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
4a: SULFATE ION (SO4a)
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Label:
No.
Name
Count
Type
Full Name
1
4LU
3
Ligand/Ion
1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-TETRAMETHYL-9,11-DIOXO-2,3,8,9,10,11-HEXAHYDRO-7H-QUINOLINO[1,8-FG]PTERIDIN-12-IUM-7-YL)-D-RIBITOL
2
MN
3
Ligand/Ion
MANGANESE (II) ION
3
NA
3
Ligand/Ion
SODIUM ION
4
SO4
1
Ligand/Ion
SULFATE ION
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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: AD1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:175 , GLU A:241 , 4LU A:502 , NA A:503
binding site for residue MN A 501
02
AC2
SOFTWARE
THR A:160 , ASN A:175 , ILE A:178 , TYR A:179 , ARG A:180 , ARG A:192 , LEU A:194 , ARG A:197 , GLY A:198 , ALA A:231 , VAL A:232 , GLU A:241 , MN A:501 , NA A:503 , HOH A:604
binding site for residue 4LU A 502
03
AC3
SOFTWARE
LEU A:176 , ALA A:231 , THR A:233 , GLU A:241 , MN A:501 , 4LU A:502 , HOH A:604
binding site for residue NA A 503
04
AC4
SOFTWARE
ASN B:175 , GLU B:241 , 4LU B:502 , NA B:503 , HOH B:610 , HOH B:615
binding site for residue MN B 501
05
AC5
SOFTWARE
THR B:160 , ASN B:175 , LEU B:176 , ILE B:178 , TYR B:179 , ARG B:180 , ARG B:192 , LEU B:194 , ARG B:197 , GLY B:198 , ALA B:231 , VAL B:232 , GLU B:241 , MN B:501 , NA B:503 , HOH B:610 , HOH B:657
binding site for residue 4LU B 502
06
AC6
SOFTWARE
LEU B:176 , ALA B:231 , GLU B:241 , MN B:501 , 4LU B:502 , HOH B:657
binding site for residue NA B 503
07
AC7
SOFTWARE
LEU B:389 , ARG B:390 , GLN B:391
binding site for residue SO4 B 504
08
AC8
SOFTWARE
ASN C:175 , GLU C:241 , 4LU C:502 , NA C:503
binding site for residue MN C 501
09
AC9
SOFTWARE
THR C:160 , ASN C:175 , LEU C:176 , ILE C:178 , TYR C:179 , ARG C:180 , ARG C:192 , LEU C:194 , ARG C:197 , GLY C:198 , ALA C:231 , VAL C:232 , GLU C:241 , THR C:320 , MN C:501 , NA C:503
binding site for residue 4LU C 502
10
AD1
SOFTWARE
LEU C:176 , ALA C:231 , GLU C:241 , MN C:501 , 4LU C:502
binding site for residue NA C 503
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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Exons
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Asym.Unit (474 KB)
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