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3PN3
Biol. Unit 3
Info
Asym.Unit (132 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (125 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PETIDE DEFORMYLASE 1B (ATPDF1B) IN COMPLEX WITH INHIBITOR 21
Authors
:
S. Fieulaine, T. Meinnel, C. Giglione
Date
:
18 Nov 10 (Deposition) - 08 Jun 11 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Peptide Deformylase, 1B, Pdf, N-Terminal Excision Pathway, Nme, Induced-Fit, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
S. Fieulaine, A. Boularot, I. Artaud, M. Desmadril, F. Dardel, T. Meinnel, C. Giglione
Trapping Conformational States Along Ligand-Binding Dynamic Of Peptide Deformylase: The Impact Of Induced Fit On Enzyme Catalysis.
Plos Biol. V. 9 E1001 2011
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: TERT-BUTYL {(2S)-1-[FORMYL(HYDROXY... (PN3a)
1b: TERT-BUTYL {(2S)-1-[FORMYL(HYDROXY... (PN3b)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
2k: ZINC ION (ZNk)
2l: ZINC ION (ZNl)
2m: ZINC ION (ZNm)
2n: ZINC ION (ZNn)
2o: ZINC ION (ZNo)
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No.
Name
Count
Type
Full Name
1
PN3
2
Ligand/Ion
TERT-BUTYL {(2S)-1-[FORMYL(HYDROXY)AMINO]-3-PHENYLPROPAN-2-YL}CARBAMATE
2
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(17, 17)
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)
17: BC8 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:18 , ASP A:19 , ASN A:74 , TYR A:80 , VAL A:102 , PRO A:104 , ARG A:112 , ARG A:146 , ZN A:1014 , HOH A:1036 , HOH A:1360 , HOH A:1553 , HOH A:1554 , HOH A:1555 , HOH A:1556
BINDING SITE FOR RESIDUE PN3 A 194
02
AC2
SOFTWARE
GLN A:48 , CYS A:91 , HIS A:133 , HIS A:137 , ZN A:1002 , HOH A:1312
BINDING SITE FOR RESIDUE ZN A 1001
03
AC3
SOFTWARE
GLN A:48 , GLU A:134 , ZN A:1001 , HOH A:1043 , HOH A:1312
BINDING SITE FOR RESIDUE ZN A 1002
04
AC4
SOFTWARE
ASP A:40 , GLU A:63 , HOH A:1040 , HOH A:1315 , HOH A:1316
BINDING SITE FOR RESIDUE ZN A 1005
05
AC5
SOFTWARE
GLU A:160 , GLU A:179 , ZN A:1012 , HOH A:1319 , GLU B:66
BINDING SITE FOR RESIDUE ZN A 1007
06
AC6
SOFTWARE
ASP A:30 , ASP A:34 , ZN A:1010 , HOH A:1328 , GLU B:69
BINDING SITE FOR RESIDUE ZN A 1009
07
AC7
SOFTWARE
ASP A:34 , ZN A:1009 , HOH A:1328 , ASP B:34 , ZN B:1011 , HOH B:1330
BINDING SITE FOR RESIDUE ZN A 1010
08
AC8
SOFTWARE
MET A:1 , GLU A:157 , GLU A:160 , ZN A:1007 , HOH A:1319 , GLU B:66
BINDING SITE FOR RESIDUE ZN A 1012
09
AC9
SOFTWARE
PN3 A:194 , HOH A:1553 , HOH A:1554 , HOH A:1555 , HOH A:1556
BINDING SITE FOR RESIDUE ZN A 1014
10
BC1
SOFTWARE
ILE B:18 , ASP B:19 , ASN B:74 , TYR B:80 , VAL B:102 , PRO B:104 , ARG B:112 , ARG B:146 , ZN B:1015 , HOH B:1196 , HOH B:1498 , HOH B:1557 , HOH B:1558 , HOH B:1559 , HOH B:1560
BINDING SITE FOR RESIDUE PN3 B 194
11
BC2
SOFTWARE
GLN B:48 , CYS B:91 , HIS B:133 , HIS B:137 , ZN B:1004 , HOH B:1313
BINDING SITE FOR RESIDUE ZN B 1003
12
BC3
SOFTWARE
GLN B:48 , GLU B:134 , ZN B:1003 , HOH B:1079 , HOH B:1313
BINDING SITE FOR RESIDUE ZN B 1004
13
BC4
SOFTWARE
ASP B:40 , GLU B:63 , HOH B:1094 , HOH B:1297 , HOH B:1318
BINDING SITE FOR RESIDUE ZN B 1006
14
BC5
SOFTWARE
GLU A:66 , GLU B:160 , GLU B:179 , ZN B:1013 , HOH B:1324
BINDING SITE FOR RESIDUE ZN B 1008
15
BC6
SOFTWARE
GLU A:69 , ZN A:1010 , ASP B:30 , ASP B:34 , HOH B:1330
BINDING SITE FOR RESIDUE ZN B 1011
16
BC7
SOFTWARE
GLU A:66 , MET B:1 , GLU B:157 , GLU B:160 , ZN B:1008 , HOH B:1324
BINDING SITE FOR RESIDUE ZN B 1013
17
BC8
SOFTWARE
PN3 B:194 , HOH B:1557 , HOH B:1558 , HOH B:1559 , HOH B:1560
BINDING SITE FOR RESIDUE ZN B 1015
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SAPs(SNPs)/Variants
(0, 0)
Info
(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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SCOP Domains
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CATH Domains
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Pep_deformylase_3pn3B01 (B:3-153)
1b: PFAM_Pep_deformylase_3pn3B02 (B:3-153)
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Clan
:
no clan defined [family: Pep_deformylase]
(48)
Family
:
Pep_deformylase
(48)
Arabidopsis thaliana (Mouse-ear cress)
(13)
1a
Pep_deformylase-3pn3B01
B:3-153
1b
Pep_deformylase-3pn3B02
B:3-153
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Asymmetric Unit 1
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Asym.Unit (132 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (64 KB)
Header - Biol.Unit 2
Biol.Unit 3 (125 KB)
Header - Biol.Unit 3
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