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1JYM
Asym. Unit
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Asym.Unit (306 KB)
Biol.Unit 1 (297 KB)
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(1)
Title
:
CRYSTALS OF PEPTIDE DEFORMYLASE FROM PLASMODIUM FALCIPARUM WITH TEN SUBUNITS PER ASYMMETRIC UNIT REVEAL CRITICAL CHARACTERISTICS OF THE ACTIVE SITE FOR DRUG DESIGN
Authors
:
A. Kumar, K. T. Nguyen, S. Srivathsan, B. Ornstein, S. Turley, I. Hirsh, D. Pei, W. G. J. Hol
Date
:
12 Sep 01 (Deposition) - 13 Mar 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Pdf, Malaria, Plasmodium, Deformylation, Metalloenzyme, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kumar, K. T. Nguyen, S. Srivathsan, B. Ornstein, S. Turley, I. Hirsh, D. Pei, W. G. Hol
Crystals Of Peptide Deformylase From Plasmodium Falciparum Reveal Critical Characteristics Of The Active Site For Drug Design.
Structure V. 10 357 2002
(for further references see the
PDB file header
)
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Hetero Components
(2, 40)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
1e: COBALT (II) ION (COe)
1f: COBALT (II) ION (COf)
1g: COBALT (II) ION (COg)
1h: COBALT (II) ION (COh)
1i: COBALT (II) ION (COi)
1j: COBALT (II) ION (COj)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO
10
Ligand/Ion
COBALT (II) ION
2
MSE
30
Mod. Amino Acid
SELENOMETHIONINE
[
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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: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:111 , CYS A:155 , HIS A:196 , HIS A:200 , HOH A:9319
BINDING SITE FOR RESIDUE CO A 300
02
AC2
SOFTWARE
GLN B:111 , CYS B:155 , HIS B:196 , HIS B:200 , HOH B:9320
BINDING SITE FOR RESIDUE CO B 1300
03
AC3
SOFTWARE
GLN C:111 , CYS C:155 , HIS C:196 , HIS C:200 , HOH C:9321
BINDING SITE FOR RESIDUE CO C 2300
04
AC4
SOFTWARE
GLN D:111 , CYS D:155 , HIS D:196 , HIS D:200 , HOH D:9322
BINDING SITE FOR RESIDUE CO D 3300
05
AC5
SOFTWARE
GLN E:111 , CYS E:155 , HIS E:196 , HIS E:200 , HOH E:9323
BINDING SITE FOR RESIDUE CO E 4300
06
AC6
SOFTWARE
GLN F:111 , CYS F:155 , HIS F:196 , GLU F:197 , HIS F:200 , HOH F:9324
BINDING SITE FOR RESIDUE CO F 5300
07
AC7
SOFTWARE
GLN G:111 , CYS G:155 , HIS G:196 , HIS G:200 , HOH G:9325
BINDING SITE FOR RESIDUE CO G 6300
08
AC8
SOFTWARE
GLN H:111 , CYS H:155 , HIS H:196 , HIS H:200 , HOH H:9326
BINDING SITE FOR RESIDUE CO H 7300
09
AC9
SOFTWARE
GLN I:111 , CYS I:155 , HIS I:196 , HIS I:200 , HOH I:9327
BINDING SITE FOR RESIDUE CO I 8300
10
BC1
SOFTWARE
GLN J:111 , CYS J:155 , HIS J:196 , HIS J:200 , HOH J:9328
BINDING SITE FOR RESIDUE CO J 9300
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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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
(1, 10)
Info
All SCOP Domains
1a: SCOP_d1jyma_ (A:)
1b: SCOP_d1jymb_ (B:)
1c: SCOP_d1jymc_ (C:)
1d: SCOP_d1jymd_ (D:)
1e: SCOP_d1jyme_ (E:)
1f: SCOP_d1jymf_ (F:)
1g: SCOP_d1jymg_ (G:)
1h: SCOP_d1jymh_ (H:)
1i: SCOP_d1jymi_ (I:)
1j: SCOP_d1jymj_ (J:)
View:
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)
(
)
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(
)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Peptide deformylase
(87)
Superfamily
:
Peptide deformylase
(87)
Family
:
Peptide deformylase
(62)
Protein domain
:
Peptide deformylase
(50)
Malaria parasite (Plasmodium falciparum) [TaxId: 5833]
(3)
1a
d1jyma_
A:
1b
d1jymb_
B:
1c
d1jymc_
C:
1d
d1jymd_
D:
1e
d1jyme_
E:
1f
d1jymf_
F:
1g
d1jymg_
G:
1h
d1jymh_
H:
1i
d1jymi_
I:
1j
d1jymj_
J:
[
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CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_1jymE00 (E:63-238)
1b: CATH_1jymA00 (A:63-241)
1c: CATH_1jymB00 (B:63-241)
1d: CATH_1jymC00 (C:64-231)
1e: CATH_1jymD00 (D:64-236)
1f: CATH_1jymH00 (H:64-236)
1g: CATH_1jymF00 (F:64-235)
1h: CATH_1jymG00 (G:63-234)
1i: CATH_1jymI00 (I:63-234)
1j: CATH_1jymJ00 (J:63-234)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Peptide Deformylase
(68)
Homologous Superfamily
:
Peptide Deformylase
(68)
Malaria parasite p (Plasmodium falciparum)
(2)
1a
1jymE00
E:63-238
1b
1jymA00
A:63-241
1c
1jymB00
B:63-241
1d
1jymC00
C:64-231
1e
1jymD00
D:64-236
1f
1jymH00
H:64-236
1g
1jymF00
F:64-235
1h
1jymG00
G:63-234
1i
1jymI00
I:63-234
1j
1jymJ00
J:63-234
[
close CATH info
]
Pfam Domains
(1, 10)
Info
all PFAM domains
1a: PFAM_Pep_deformylase_1jymJ01 (J:64-216)
1b: PFAM_Pep_deformylase_1jymJ02 (J:64-216)
1c: PFAM_Pep_deformylase_1jymJ03 (J:64-216)
1d: PFAM_Pep_deformylase_1jymJ04 (J:64-216)
1e: PFAM_Pep_deformylase_1jymJ05 (J:64-216)
1f: PFAM_Pep_deformylase_1jymJ06 (J:64-216)
1g: PFAM_Pep_deformylase_1jymJ07 (J:64-216)
1h: PFAM_Pep_deformylase_1jymJ08 (J:64-216)
1i: PFAM_Pep_deformylase_1jymJ09 (J:64-216)
1j: PFAM_Pep_deformylase_1jymJ10 (J:64-216)
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Clans
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(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Pep_deformylase]
(48)
Family
:
Pep_deformylase
(48)
Plasmodium falciparum (isolate 3D7)
(3)
1a
Pep_deformylase-1jymJ01
J:64-216
1b
Pep_deformylase-1jymJ02
J:64-216
1c
Pep_deformylase-1jymJ03
J:64-216
1d
Pep_deformylase-1jymJ04
J:64-216
1e
Pep_deformylase-1jymJ05
J:64-216
1f
Pep_deformylase-1jymJ06
J:64-216
1g
Pep_deformylase-1jymJ07
J:64-216
1h
Pep_deformylase-1jymJ08
J:64-216
1i
Pep_deformylase-1jymJ09
J:64-216
1j
Pep_deformylase-1jymJ10
J:64-216
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