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2NX3
Biol. Unit 1
Info
Asym.Unit (542 KB)
Biol.Unit 1 (185 KB)
Biol.Unit 2 (183 KB)
Biol.Unit 3 (184 KB)
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(1)
Title
:
STRUCTURAL AND MECHANISTIC CHANGES ALONG AN ENGINEERED PATH FROM METALLO TO NON-METALLO KDO8P SYNTHASE
Authors
:
F. Kona, X. Xu, P. Martin, P. Kuzmic, D. L. Gatti
Date
:
16 Nov 06 (Deposition) - 24 Apr 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Keywords
:
Kdo, Kdo8P, Kdo8Ps, Pep, A5P, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Kona, X. Xu, P. Martin, P. Kuzmic, D. L. Gatti
Structural And Mechanistic Changes Along An Engineered Path From Metallo To Nonmetallo 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthases.
Biochemistry V. 46 4532 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: (2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHY... (1NTa)
2a: ARABINOSE-5-PHOSPHATE (A5Pa)
2b: ARABINOSE-5-PHOSPHATE (A5Pb)
2c: ARABINOSE-5-PHOSPHATE (A5Pc)
2d: ARABINOSE-5-PHOSPHATE (A5Pd)
2e: ARABINOSE-5-PHOSPHATE (A5Pe)
2f: ARABINOSE-5-PHOSPHATE (A5Pf)
2g: ARABINOSE-5-PHOSPHATE (A5Pg)
2h: ARABINOSE-5-PHOSPHATE (A5Ph)
2i: ARABINOSE-5-PHOSPHATE (A5Pi)
2j: ARABINOSE-5-PHOSPHATE (A5Pj)
2k: ARABINOSE-5-PHOSPHATE (A5Pk)
3a: PHOSPHOENOLPYRUVATE (PEPa)
3b: PHOSPHOENOLPYRUVATE (PEPb)
3c: PHOSPHOENOLPYRUVATE (PEPc)
3d: PHOSPHOENOLPYRUVATE (PEPd)
3e: PHOSPHOENOLPYRUVATE (PEPe)
3f: PHOSPHOENOLPYRUVATE (PEPf)
3g: PHOSPHOENOLPYRUVATE (PEPg)
3h: PHOSPHOENOLPYRUVATE (PEPh)
3i: PHOSPHOENOLPYRUVATE (PEPi)
3j: PHOSPHOENOLPYRUVATE (PEPj)
3k: PHOSPHOENOLPYRUVATE (PEPk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1NT
1
Ligand/Ion
(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC ACID
2
A5P
3
Ligand/Ion
ARABINOSE-5-PHOSPHATE
3
PEP
3
Ligand/Ion
PHOSPHOENOLPYRUVATE
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: BC3 (SOFTWARE)
5: BC4 (SOFTWARE)
6: BC5 (SOFTWARE)
7: BC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:41 , SER A:43 , LYS A:46 , ASP A:81 , GLN A:99 , PRO A:101 , ALA A:102 , LYS A:124 , ARG A:154 , HIS A:185 , PHE A:220 , GLU A:222 , A5P A:269 , HOH A:277 , HOH A:283 , HOH A:293
BINDING SITE FOR RESIDUE PEP A 268
2
AC2
SOFTWARE
LYS B:41 , SER B:43 , LYS B:46 , GLN B:99 , PRO B:101 , ALA B:102 , LYS B:124 , ARG B:154 , HIS B:185 , PHE B:220 , A5P B:269 , HOH B:270 , HOH B:275 , HOH B:281
BINDING SITE FOR RESIDUE PEP B 268
3
AC3
SOFTWARE
ASN C:11 , LYS C:41 , SER C:43 , LYS C:46 , GLN C:99 , PRO C:101 , ALA C:102 , LYS C:124 , ARG C:154 , HIS C:185 , GLU C:222 , A5P C:269 , HOH C:289 , HOH C:293 , HOH C:295
BINDING SITE FOR RESIDUE PEP C 268
4
BC3
SOFTWARE
ASN A:11 , LYS A:46 , ASN A:48 , ARG A:49 , SER A:50 , HIS A:185 , GLN A:188 , LYS A:196 , SER A:197 , ASP A:233 , PEP A:268 , HOH A:278 , HOH A:362 , HOH A:393 , ARG B:106
BINDING SITE FOR RESIDUE A5P A 269
5
BC4
SOFTWARE
ARG A:106 , ASN B:11 , LYS B:46 , ASN B:48 , ARG B:49 , SER B:50 , HIS B:185 , GLN B:188 , LYS B:196 , SER B:197 , ASP B:233 , PEP B:268 , HOH B:286 , HOH B:435
BINDING SITE FOR RESIDUE A5P B 269
6
BC5
SOFTWARE
ASN C:11 , LYS C:46 , ASN C:48 , ARG C:49 , SER C:50 , HIS C:185 , GLN C:188 , LYS C:196 , SER C:197 , ASP C:233 , PEP C:268 , HOH C:308 , ARG D:106
BINDING SITE FOR RESIDUE A5P C 269
7
BC6
SOFTWARE
ARG C:106 , ASN D:11 , LYS D:41 , SER D:43 , LYS D:46 , ASN D:48 , ARG D:49 , SER D:50 , GLN D:99 , PRO D:101 , ALA D:102 , LYS D:124 , ARG D:154 , HIS D:185 , LYS D:196 , SER D:197 , GLU D:222 , ASP D:233 , HOH D:277 , HOH D:289 , HOH D:344
BINDING SITE FOR RESIDUE 1NT D 268
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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
(, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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
(1, 12)
Info
All SCOP Domains
1a: SCOP_d2nx3a_ (A:)
1b: SCOP_d2nx3b_ (B:)
1c: SCOP_d2nx3c_ (C:)
1d: SCOP_d2nx3d_ (D:)
1e: SCOP_d2nx3e_ (E:)
1f: SCOP_d2nx3f_ (F:)
1g: SCOP_d2nx3g_ (G:)
1h: SCOP_d2nx3h_ (H:)
1i: SCOP_d2nx3i_ (I:)
1j: SCOP_d2nx3j_ (J:)
1k: SCOP_d2nx3k_ (K:)
1l: SCOP_d2nx3l_ (L:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
Class I DAHP synthetase
(87)
Protein domain
:
3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)
(44)
Aquifex aeolicus [TaxId: 63363]
(32)
1a
d2nx3a_
A:
1b
d2nx3b_
B:
1c
d2nx3c_
C:
1d
d2nx3d_
D:
1e
d2nx3e_
E:
1f
d2nx3f_
F:
1g
d2nx3g_
G:
1h
d2nx3h_
H:
1i
d2nx3i_
I:
1j
d2nx3j_
J:
1k
d2nx3k_
K:
1l
d2nx3l_
L:
[
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]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2nx3A00 (A:3-264)
1b: CATH_2nx3B00 (B:3-264)
1c: CATH_2nx3C00 (C:3-264)
1d: CATH_2nx3D00 (D:3-264)
1e: CATH_2nx3E00 (E:3-264)
1f: CATH_2nx3F00 (F:3-264)
1g: CATH_2nx3G00 (G:3-264)
1h: CATH_2nx3H00 (H:3-264)
1i: CATH_2nx3I00 (I:3-264)
1j: CATH_2nx3J00 (J:3-264)
1k: CATH_2nx3K00 (K:3-264)
1l: CATH_2nx3L00 (L:3-264)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Aquifex aeolicus. Organism_taxid: 63363.
(20)
1a
2nx3A00
A:3-264
1b
2nx3B00
B:3-264
1c
2nx3C00
C:3-264
1d
2nx3D00
D:3-264
1e
2nx3E00
E:3-264
1f
2nx3F00
F:3-264
1g
2nx3G00
G:3-264
1h
2nx3H00
H:3-264
1i
2nx3I00
I:3-264
1j
2nx3J00
J:3-264
1k
2nx3K00
K:3-264
1l
2nx3L00
L:3-264
[
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_DAHP_synth_1_2nx3L01 (L:3-259)
1b: PFAM_DAHP_synth_1_2nx3L02 (L:3-259)
1c: PFAM_DAHP_synth_1_2nx3L03 (L:3-259)
1d: PFAM_DAHP_synth_1_2nx3L04 (L:3-259)
1e: PFAM_DAHP_synth_1_2nx3L05 (L:3-259)
1f: PFAM_DAHP_synth_1_2nx3L06 (L:3-259)
1g: PFAM_DAHP_synth_1_2nx3L07 (L:3-259)
1h: PFAM_DAHP_synth_1_2nx3L08 (L:3-259)
1i: PFAM_DAHP_synth_1_2nx3L09 (L:3-259)
1j: PFAM_DAHP_synth_1_2nx3L10 (L:3-259)
1k: PFAM_DAHP_synth_1_2nx3L11 (L:3-259)
1l: PFAM_DAHP_synth_1_2nx3L12 (L:3-259)
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
DAHP_synth_1
(46)
Aquifex aeolicus
(17)
1a
DAHP_synth_1-2nx3L01
L:3-259
1b
DAHP_synth_1-2nx3L02
L:3-259
1c
DAHP_synth_1-2nx3L03
L:3-259
1d
DAHP_synth_1-2nx3L04
L:3-259
1e
DAHP_synth_1-2nx3L05
L:3-259
1f
DAHP_synth_1-2nx3L06
L:3-259
1g
DAHP_synth_1-2nx3L07
L:3-259
1h
DAHP_synth_1-2nx3L08
L:3-259
1i
DAHP_synth_1-2nx3L09
L:3-259
1j
DAHP_synth_1-2nx3L10
L:3-259
1k
DAHP_synth_1-2nx3L11
L:3-259
1l
DAHP_synth_1-2nx3L12
L:3-259
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Asym.Unit (542 KB)
Header - Asym.Unit
Biol.Unit 1 (185 KB)
Header - Biol.Unit 1
Biol.Unit 2 (183 KB)
Header - Biol.Unit 2
Biol.Unit 3 (184 KB)
Header - Biol.Unit 3
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