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1RF4
Asym. Unit
Info
Asym.Unit (281 KB)
Biol.Unit 1 (74 KB)
Biol.Unit 2 (74 KB)
Biol.Unit 3 (73 KB)
Biol.Unit 4 (73 KB)
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(1)
Title
:
STRUCTURAL STUDIES OF STREPTOCOCCUS PNEUMONIAE EPSP SYNTHASE, TETRAHEDRAL INTERMEDIATE BOUND STATE
Authors
:
H. Park, J. L. Hilsenbeck, H. J. Kim, W. A. Shuttleworth, Y. H. Park, J. N. Evans, C. Kang
Date
:
07 Nov 03 (Deposition) - 17 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Shikimate Pathway, Epsp Synthase, S3P, Glyphosate, Pep, S. Pneumoniae, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Park, J. L. Hilsenbeck, H. J. Kim, W. A. Shuttleworth, Y. H. Park, J. N. Evans, C. Kang
Structural Studies Of Streptococcus Pneumoniae Epsp Synthase In Unliganded State, Tetrahedral Intermediate-Bound State And S3P-Glp-Bound State.
Mol. Microbiol. V. 51 963 2004
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: (3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FL... (SPQa)
1b: (3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FL... (SPQb)
1c: (3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FL... (SPQc)
1d: (3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FL... (SPQd)
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No.
Name
Count
Type
Full Name
1
SPQ
4
Ligand/Ion
(3R,4S,5R)-5-{[(1R)-1-CARBOXY-2-FLUORO-1-(PHOSPHONOOXY)ETHYL]OXY}-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:20 , SER A:21 , ARG A:25 , GLY A:92 , THR A:93 , ARG A:120 , SER A:166 , ALA A:167 , GLN A:168 , ARG A:193 , ASP A:312 , LYS A:339 , GLU A:340 , ARG A:343 , HIS A:384 , ARG A:385 , HOH A:1453 , HOH A:1456 , HOH A:1472 , HOH A:1481 , HOH A:1505 , HOH A:1581 , HOH A:1658
BINDING SITE FOR RESIDUE SPQ A 1451
2
AC2
SOFTWARE
LYS B:20 , SER B:21 , ARG B:25 , GLY B:92 , THR B:93 , ARG B:120 , SER B:166 , ALA B:167 , GLN B:168 , ARG B:193 , ASP B:312 , LYS B:339 , GLU B:340 , ARG B:343 , HIS B:384 , ARG B:385 , HOH B:1560 , HOH B:1593 , HOH B:1601 , HOH B:1602 , HOH B:1617 , HOH B:1682
BINDING SITE FOR RESIDUE SPQ B 1551
3
AC3
SOFTWARE
LYS C:20 , SER C:21 , ARG C:25 , SER C:91 , GLY C:92 , THR C:93 , ARG C:120 , SER C:166 , ALA C:167 , GLN C:168 , ARG C:193 , ILE C:311 , ASP C:312 , LYS C:339 , GLU C:340 , ARG C:343 , HIS C:384 , ARG C:385 , HOH C:1652 , HOH C:1669 , HOH C:1678 , HOH C:1694 , HOH C:1734 , HOH C:1762
BINDING SITE FOR RESIDUE SPQ C 1651
4
AC4
SOFTWARE
LYS D:20 , SER D:21 , ARG D:25 , GLY D:92 , THR D:93 , ARG D:120 , SER D:166 , ALA D:167 , GLN D:168 , ARG D:193 , ASP D:312 , LYS D:339 , GLU D:340 , ARG D:343 , HIS D:384 , ARG D:385 , HOH D:1761 , HOH D:1771 , HOH D:1777 , HOH D:1783 , HOH D:1821 , HOH D:1900
BINDING SITE FOR RESIDUE SPQ D 1751
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: EPSP_SYNTHASE_1 (A:86-100,B:86-100,C:86-100,D:86-10...)
2: EPSP_SYNTHASE_2 (A:337-355,B:337-355,C:337-355,D:33...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EPSP_SYNTHASE_1
PS00104
EPSP synthase signature 1.
AROA_STRPN
86-100
4
A:86-100
B:86-100
C:86-100
D:86-100
2
EPSP_SYNTHASE_2
PS00885
EPSP synthase signature 2.
AROA_STRPN
337-355
4
A:337-355
B:337-355
C:337-355
D:337-355
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Exons
(0, 0)
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1rf4a_ (A:)
1b: SCOP_d1rf4b_ (B:)
1c: SCOP_d1rf4c_ (C:)
1d: SCOP_d1rf4d_ (D:)
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Protein Domains
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)
(
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
IF3-like
(127)
Superfamily
:
EPT/RTPC-like
(82)
Family
:
Enolpyruvate transferase, EPT
(68)
Protein domain
:
5-enol-pyruvyl shikimate-3-phosphate (EPSP) synthase
(26)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(3)
1a
d1rf4a_
A:
1b
d1rf4b_
B:
1c
d1rf4c_
C:
1d
d1rf4d_
D:
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1rf4A02 (A:20-229)
1b: CATH_1rf4A01 (A:1-19,A:230-427)
1c: CATH_1rf4B01 (B:1-19,B:230-427)
1d: CATH_1rf4C01 (C:1-19,C:230-427)
1e: CATH_1rf4D01 (D:1-19,D:230-427)
1f: CATH_1rf4B02 (B:20-229)
1g: CATH_1rf4C02 (C:20-229)
1h: CATH_1rf4D02 (D:20-229)
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Organisms
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(
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-beta prism
(50)
Topology
:
UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
(50)
Homologous Superfamily
:
[code=3.65.10.10, no name defined]
(47)
Streptococcus pneumoniae. Organism_taxid: 1313.
(3)
1a
1rf4A02
A:20-229
1b
1rf4A01
A:1-19,A:230-427
1c
1rf4B01
B:1-19,B:230-427
1d
1rf4C01
C:1-19,C:230-427
1e
1rf4D01
D:1-19,D:230-427
1f
1rf4B02
B:20-229
1g
1rf4C02
C:20-229
1h
1rf4D02
D:20-229
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_EPSP_synthase_1rf4D01 (D:4-421)
1b: PFAM_EPSP_synthase_1rf4D02 (D:4-421)
1c: PFAM_EPSP_synthase_1rf4D03 (D:4-421)
1d: PFAM_EPSP_synthase_1rf4D04 (D:4-421)
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)
Clan
:
EPT_RTPC
(43)
Family
:
EPSP_synthase
(40)
Streptococcus pneumoniae
(3)
1a
EPSP_synthase-1rf4D01
D:4-421
1b
EPSP_synthase-1rf4D02
D:4-421
1c
EPSP_synthase-1rf4D03
D:4-421
1d
EPSP_synthase-1rf4D04
D:4-421
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (281 KB)
Header - Asym.Unit
Biol.Unit 1 (74 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 KB)
Header - Biol.Unit 2
Biol.Unit 3 (73 KB)
Header - Biol.Unit 3
Biol.Unit 4 (73 KB)
Header - Biol.Unit 4
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