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4MZY
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (172 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS NICOTINATE PHOSPHORIBOSYLTRANSFERASE WITH MALONATE AND PHOSPHATE BOUND
Authors
:
Y. Patskovsky, R. Toro, S. R. Wasserman, S. C. Almo, S. K. Burley, New Yo Research Center For Structural Genomics (Nysgxrc), New York Structural Genomics Research Consortium (Nysgrc)
Date
:
30 Sep 13 (Deposition) - 23 Oct 13 (Release) - 29 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Transferase, Structural Genomics, Psi, Rotein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, New York Structural Genomics Research Consortium, Nysgrc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Patskovsky, R. Toro, S. R. Wasserman, S. K. Burley, S. C. Almo
Crystal Structure Of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase
To Be Published
[
close entry info
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Hetero Components
(5, 22)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: FORMIC ACID (FMTa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
4a: MALONIC ACID (MLAa)
4b: MALONIC ACID (MLAb)
4c: MALONIC ACID (MLAc)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
FMT
1
Ligand/Ion
FORMIC ACID
3
GOL
12
Ligand/Ion
GLYCEROL
4
MLA
3
Ligand/Ion
MALONIC ACID
5
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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Sites
(22, 22)
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)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:225 , ARG A:226 , ASP A:227 , HOH A:725 , HOH A:726
BINDING SITE FOR RESIDUE PO4 A 501
02
AC2
SOFTWARE
PHE A:160 , ASN A:293 , ASP A:294 , GLY A:316 , THR A:317 , HOH A:630 , HOH A:654 , HOH A:722 , HOH A:723
BINDING SITE FOR RESIDUE PO4 A 502
03
AC3
SOFTWARE
TYR A:179 , ILE A:180 , GLY A:181 , GLY A:182 , LYS A:437 , LEU A:444 , HOH A:685
BINDING SITE FOR RESIDUE GOL A 503
04
AC4
SOFTWARE
GLU A:104 , TYR A:428 , PRO A:431 , TYR A:439 , HOH A:666
BINDING SITE FOR RESIDUE GOL A 504
05
AC5
SOFTWARE
MET A:396 , HIS A:398 , LYS A:406 , PRO A:461 , ASP A:463 , GOL A:513
BINDING SITE FOR RESIDUE GOL A 505
06
AC6
SOFTWARE
SER A:150 , ARG A:453 , ASP A:454 , LEU A:455
BINDING SITE FOR RESIDUE GOL A 506
07
AC7
SOFTWARE
ASP A:236 , LEU A:238 , LYS A:239 , HOH A:658
BINDING SITE FOR RESIDUE GOL A 507
08
AC8
SOFTWARE
ASP A:85 , GLN A:364 , TRP A:384 , GLU A:386 , ASP A:387 , ARG A:389
BINDING SITE FOR RESIDUE GOL A 508
09
AC9
SOFTWARE
GLY A:212 , ASN A:213 , LEU A:486 , HOH A:631 , HOH A:758
BINDING SITE FOR RESIDUE GOL A 509
10
BC1
SOFTWARE
LYS A:149 , ASP A:154 , ASP A:184
BINDING SITE FOR RESIDUE GOL A 510
11
BC2
SOFTWARE
ASP A:7 , GLU A:57 , ASN A:61 , ILE A:194 , MLA A:516 , HOH A:690 , HOH A:732
BINDING SITE FOR RESIDUE GOL A 511
12
BC3
SOFTWARE
LEU A:63 , GLU A:64 , LEU A:66 , GLU A:94 , PHE A:95 , LYS A:255
BINDING SITE FOR RESIDUE GOL A 512
13
BC4
SOFTWARE
TYR A:270 , HIS A:398 , LYS A:459 , TYR A:460 , PRO A:461 , VAL A:462 , ASP A:463 , GOL A:505 , HOH A:673 , HOH A:701
BINDING SITE FOR RESIDUE GOL A 513
14
BC5
SOFTWARE
ASP A:155 , ILE A:310 , ASP A:311
BINDING SITE FOR RESIDUE GOL A 514
15
BC6
SOFTWARE
GLN A:125 , GLU A:128 , ALA A:204 , HIS A:205 , SER A:206 , LYS A:333 , FMT A:520 , HOH A:626 , HOH A:721
BINDING SITE FOR RESIDUE MLA A 515
16
BC7
SOFTWARE
ASP A:7 , ARG A:58 , ASP A:169 , TRP A:173 , ARG A:190 , GOL A:511 , HOH A:759
BINDING SITE FOR RESIDUE MLA A 516
17
BC8
SOFTWARE
GLU A:38 , TYR A:40 , PRO A:113 , THR A:359 , LYS A:363 , HOH A:714 , HOH A:730 , HOH A:761
BINDING SITE FOR RESIDUE MLA A 517
18
BC9
SOFTWARE
ARG A:163 , ARG A:164 , VAL A:331 , PHE A:332
BINDING SITE FOR RESIDUE CL A 518
19
CC1
SOFTWARE
ARG A:274
BINDING SITE FOR RESIDUE CL A 519
20
CC2
SOFTWARE
PHE A:160 , ARG A:262 , MLA A:515
BINDING SITE FOR RESIDUE FMT A 520
21
CC3
SOFTWARE
THR A:202 , HOH A:638 , HOH A:768 , HOH A:769
BINDING SITE FOR RESIDUE CL A 521
22
CC4
SOFTWARE
SER A:200 , GLY A:201 , HOH A:767 , HOH A:768
BINDING SITE FOR RESIDUE CL A 522
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info 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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All Exon Boundaries
View:
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d4mzya1 (A:3-140)
2a: SCOP_d4mzya2 (A:141-488)
View:
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Classes
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
Nicotinate/Quinolinate PRTase N-terminal domain-like
(25)
Family
:
NadC N-terminal domain-like
(13)
Protein domain
:
Putative nicotinate phosphoribosyltransferase EF2626
(2)
Enterococcus faecalis [TaxId: 1351]
(2)
1a
d4mzya1
A:3-140
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Nicotinate/Quinolinate PRTase C-terminal domain-like
(25)
Family
:
NadC C-terminal domain-like
(13)
Protein domain
:
Putative nicotinate phosphoribosyltransferase EF2626
(2)
Enterococcus faecalis [TaxId: 1351]
(2)
2a
d4mzya2
A:141-488
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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Atom Selection
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Protein
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Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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