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3C5Y
Biol. Unit 3
Info
Asym.Unit (611 KB)
Biol.Unit 1 (154 KB)
Biol.Unit 2 (162 KB)
Biol.Unit 3 (155 KB)
Biol.Unit 4 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A PUTATIVE RIBOSE 5-PHOSPHATE ISOMERASE (SARO_3514) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM AT 1.81 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
01 Feb 08 (Deposition) - 19 Feb 08 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.81
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Ribose 5-Phosphate Isomerase (Yp_001165900. 1) From Novosphingobium Aromaticivorans Dsm 12444 At 1. 81 A Resolution
To Be Published
[
close entry info
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Hetero Components
(4, 52)
Info
All Hetero Components
1a: 3-SULFINOALANINE (CSDa)
1b: 3-SULFINOALANINE (CSDb)
1c: 3-SULFINOALANINE (CSDc)
1d: 3-SULFINOALANINE (CSDd)
1e: 3-SULFINOALANINE (CSDe)
1f: 3-SULFINOALANINE (CSDf)
1g: 3-SULFINOALANINE (CSDg)
1h: 3-SULFINOALANINE (CSDh)
1i: 3-SULFINOALANINE (CSDi)
1j: 3-SULFINOALANINE (CSDj)
1k: 3-SULFINOALANINE (CSDk)
1l: 3-SULFINOALANINE (CSDl)
1m: 3-SULFINOALANINE (CSDm)
1n: 3-SULFINOALANINE (CSDn)
1o: 3-SULFINOALANINE (CSDo)
1p: 3-SULFINOALANINE (CSDp)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
2aj: 1,2-ETHANEDIOL (EDOaj)
2ak: 1,2-ETHANEDIOL (EDOak)
2al: 1,2-ETHANEDIOL (EDOal)
2am: 1,2-ETHANEDIOL (EDOam)
2an: 1,2-ETHANEDIOL (EDOan)
2ao: 1,2-ETHANEDIOL (EDOao)
2ap: 1,2-ETHANEDIOL (EDOap)
2aq: 1,2-ETHANEDIOL (EDOaq)
2ar: 1,2-ETHANEDIOL (EDOar)
2as: 1,2-ETHANEDIOL (EDOas)
2at: 1,2-ETHANEDIOL (EDOat)
2au: 1,2-ETHANEDIOL (EDOau)
2av: 1,2-ETHANEDIOL (EDOav)
2aw: 1,2-ETHANEDIOL (EDOaw)
2ax: 1,2-ETHANEDIOL (EDOax)
2ay: 1,2-ETHANEDIOL (EDOay)
2az: 1,2-ETHANEDIOL (EDOaz)
2b: 1,2-ETHANEDIOL (EDOb)
2ba: 1,2-ETHANEDIOL (EDOba)
2bb: 1,2-ETHANEDIOL (EDObb)
2bc: 1,2-ETHANEDIOL (EDObc)
2bd: 1,2-ETHANEDIOL (EDObd)
2be: 1,2-ETHANEDIOL (EDObe)
2bf: 1,2-ETHANEDIOL (EDObf)
2bg: 1,2-ETHANEDIOL (EDObg)
2bh: 1,2-ETHANEDIOL (EDObh)
2bi: 1,2-ETHANEDIOL (EDObi)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3ao: SELENOMETHIONINE (MSEao)
3ap: SELENOMETHIONINE (MSEap)
3aq: SELENOMETHIONINE (MSEaq)
3ar: SELENOMETHIONINE (MSEar)
3as: SELENOMETHIONINE (MSEas)
3at: SELENOMETHIONINE (MSEat)
3au: SELENOMETHIONINE (MSEau)
3av: SELENOMETHIONINE (MSEav)
3aw: SELENOMETHIONINE (MSEaw)
3ax: SELENOMETHIONINE (MSEax)
3ay: SELENOMETHIONINE (MSEay)
3az: SELENOMETHIONINE (MSEaz)
3b: SELENOMETHIONINE (MSEb)
3ba: SELENOMETHIONINE (MSEba)
3bb: SELENOMETHIONINE (MSEbb)
3bc: SELENOMETHIONINE (MSEbc)
3bd: SELENOMETHIONINE (MSEbd)
3be: SELENOMETHIONINE (MSEbe)
3bf: SELENOMETHIONINE (MSEbf)
3bg: SELENOMETHIONINE (MSEbg)
3bh: SELENOMETHIONINE (MSEbh)
3bi: SELENOMETHIONINE (MSEbi)
3bj: SELENOMETHIONINE (MSEbj)
3bk: SELENOMETHIONINE (MSEbk)
3bl: SELENOMETHIONINE (MSEbl)
3bm: SELENOMETHIONINE (MSEbm)
3bn: SELENOMETHIONINE (MSEbn)
3bo: SELENOMETHIONINE (MSEbo)
3bp: SELENOMETHIONINE (MSEbp)
3bq: SELENOMETHIONINE (MSEbq)
3br: SELENOMETHIONINE (MSEbr)
3bs: SELENOMETHIONINE (MSEbs)
3bt: SELENOMETHIONINE (MSEbt)
3bu: SELENOMETHIONINE (MSEbu)
3bv: SELENOMETHIONINE (MSEbv)
3bw: SELENOMETHIONINE (MSEbw)
3bx: SELENOMETHIONINE (MSEbx)
3by: SELENOMETHIONINE (MSEby)
3bz: SELENOMETHIONINE (MSEbz)
3c: SELENOMETHIONINE (MSEc)
3ca: SELENOMETHIONINE (MSEca)
3cb: SELENOMETHIONINE (MSEcb)
3cc: SELENOMETHIONINE (MSEcc)
3cd: SELENOMETHIONINE (MSEcd)
3ce: SELENOMETHIONINE (MSEce)
3cf: SELENOMETHIONINE (MSEcf)
3cg: SELENOMETHIONINE (MSEcg)
3ch: SELENOMETHIONINE (MSEch)
3ci: SELENOMETHIONINE (MSEci)
3cj: SELENOMETHIONINE (MSEcj)
3ck: SELENOMETHIONINE (MSEck)
3cl: SELENOMETHIONINE (MSEcl)
3cm: SELENOMETHIONINE (MSEcm)
3cn: SELENOMETHIONINE (MSEcn)
3co: SELENOMETHIONINE (MSEco)
3cp: SELENOMETHIONINE (MSEcp)
3cq: SELENOMETHIONINE (MSEcq)
3cr: SELENOMETHIONINE (MSEcr)
3cs: SELENOMETHIONINE (MSEcs)
3ct: SELENOMETHIONINE (MSEct)
3cu: SELENOMETHIONINE (MSEcu)
3cv: SELENOMETHIONINE (MSEcv)
3cw: SELENOMETHIONINE (MSEcw)
3cx: SELENOMETHIONINE (MSEcx)
3cy: SELENOMETHIONINE (MSEcy)
3cz: SELENOMETHIONINE (MSEcz)
3d: SELENOMETHIONINE (MSEd)
3da: SELENOMETHIONINE (MSEda)
3db: SELENOMETHIONINE (MSEdb)
3dc: SELENOMETHIONINE (MSEdc)
3dd: SELENOMETHIONINE (MSEdd)
3de: SELENOMETHIONINE (MSEde)
3df: SELENOMETHIONINE (MSEdf)
3dg: SELENOMETHIONINE (MSEdg)
3dh: SELENOMETHIONINE (MSEdh)
3di: SELENOMETHIONINE (MSEdi)
3dj: SELENOMETHIONINE (MSEdj)
3dk: SELENOMETHIONINE (MSEdk)
3dl: SELENOMETHIONINE (MSEdl)
3dm: SELENOMETHIONINE (MSEdm)
3dn: SELENOMETHIONINE (MSEdn)
3do: SELENOMETHIONINE (MSEdo)
3dp: SELENOMETHIONINE (MSEdp)
3dq: SELENOMETHIONINE (MSEdq)
3dr: SELENOMETHIONINE (MSEdr)
3ds: SELENOMETHIONINE (MSEds)
3dt: SELENOMETHIONINE (MSEdt)
3du: SELENOMETHIONINE (MSEdu)
3dv: SELENOMETHIONINE (MSEdv)
3dw: SELENOMETHIONINE (MSEdw)
3dx: SELENOMETHIONINE (MSEdx)
3dy: SELENOMETHIONINE (MSEdy)
3dz: SELENOMETHIONINE (MSEdz)
3e: SELENOMETHIONINE (MSEe)
3ea: SELENOMETHIONINE (MSEea)
3eb: SELENOMETHIONINE (MSEeb)
3ec: SELENOMETHIONINE (MSEec)
3ed: SELENOMETHIONINE (MSEed)
3ee: SELENOMETHIONINE (MSEee)
3ef: SELENOMETHIONINE (MSEef)
3eg: SELENOMETHIONINE (MSEeg)
3eh: SELENOMETHIONINE (MSEeh)
3ei: SELENOMETHIONINE (MSEei)
3ej: SELENOMETHIONINE (MSEej)
3ek: SELENOMETHIONINE (MSEek)
3el: SELENOMETHIONINE (MSEel)
3em: SELENOMETHIONINE (MSEem)
3en: SELENOMETHIONINE (MSEen)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: NITRATE ION (NO3a)
4b: NITRATE ION (NO3b)
4c: NITRATE ION (NO3c)
4d: NITRATE ION (NO3d)
4e: NITRATE ION (NO3e)
4f: NITRATE ION (NO3f)
4g: NITRATE ION (NO3g)
4h: NITRATE ION (NO3h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSD
4
Mod. Amino Acid
3-SULFINOALANINE
2
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
3
MSE
36
Mod. Amino Acid
SELENOMETHIONINE
4
NO3
1
Ligand/Ion
NITRATE ION
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: CC4 (SOFTWARE)
05: FC6 (SOFTWARE)
06: FC7 (SOFTWARE)
07: FC8 (SOFTWARE)
08: FC9 (SOFTWARE)
09: GC1 (SOFTWARE)
10: GC2 (SOFTWARE)
11: GC3 (SOFTWARE)
12: GC4 (SOFTWARE)
13: GC5 (SOFTWARE)
14: GC6 (SOFTWARE)
15: GC7 (SOFTWARE)
16: HC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
TYR G:195 , ARG G:208 , NO3 G:214 , HOH G:329 , HOH G:434 , TYR J:195 , PRO J:196 , ARG J:208
BINDING SITE FOR RESIDUE NO3 G 213
02
AC6
SOFTWARE
ALA G:191 , TYR G:195 , ARG G:208 , NO3 G:213 , HOH G:426 , HOH G:427 , ALA J:191 , TYR J:195 , ARG J:208
BINDING SITE FOR RESIDUE NO3 G 214
03
AC7
SOFTWARE
GLY I:0 , GLY I:30 , LYS I:32
BINDING SITE FOR RESIDUE NO3 I 213
04
CC4
SOFTWARE
ASP B:177 , GLN B:178 , HOH B:261 , HOH B:379 , HOH G:235 , EDO J:215
BINDING SITE FOR RESIDUE EDO B 218
05
FC6
SOFTWARE
PHE I:89 , ASN I:106 , ARG I:155 , LEU I:158 , ARG I:159 , HOH I:251
BINDING SITE FOR RESIDUE EDO I 214
06
FC7
SOFTWARE
PHE I:100 , LYS I:133 , HOH I:225 , HOH I:256 , ASP L:129
BINDING SITE FOR RESIDUE EDO I 215
07
FC8
SOFTWARE
LYS I:117 , GLY I:118 , HOH I:323 , HOH I:398 , GLY K:118 , HOH K:364
BINDING SITE FOR RESIDUE EDO I 216
08
FC9
SOFTWARE
LYS I:2 , PRO I:196 , ASN I:197 , HOH I:258 , HOH I:315
BINDING SITE FOR RESIDUE EDO I 217
09
GC1
SOFTWARE
HOH I:292 , PHE J:89 , ASN J:106 , ARG J:155 , ARG J:159
BINDING SITE FOR RESIDUE EDO J 213
10
GC2
SOFTWARE
ASP J:168 , LEU J:170 , THR J:171 , LYS J:174 , ARG O:167
BINDING SITE FOR RESIDUE EDO J 214
11
GC3
SOFTWARE
EDO B:218 , ASN G:205 , TYR G:206 , HOH G:232 , LYS J:189 , GLU J:192
BINDING SITE FOR RESIDUE EDO J 215
12
GC4
SOFTWARE
PHE K:89 , ASN K:106 , ARG K:155 , ARG K:159 , HOH K:236
BINDING SITE FOR RESIDUE EDO K 213
13
GC5
SOFTWARE
HOH J:329 , PHE K:100 , LYS K:133 , HOH K:315
BINDING SITE FOR RESIDUE EDO K 214
14
GC6
SOFTWARE
ASN J:126 , ASP K:95 , HOH K:334 , HOH K:349
BINDING SITE FOR RESIDUE EDO K 215
15
GC7
SOFTWARE
PHE L:89 , ASN L:106 , ARG L:155 , ARG L:159 , HOH L:220
BINDING SITE FOR RESIDUE EDO L 213
16
HC2
SOFTWARE
THR L:175 , ASP M:168 , LEU M:170 , THR M:171 , LYS M:174
BINDING SITE FOR RESIDUE EDO M 216
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_3c5yA00 (A:0-210)
1b: CATH_3c5yD00 (D:0-210)
1c: CATH_3c5yM00 (M:0-211)
1d: CATH_3c5yN00 (N:0-211)
1e: CATH_3c5yF00 (F:-1-211)
1f: CATH_3c5yL00 (L:0-212)
1g: CATH_3c5yH00 (H:-3-210)
1h: CATH_3c5yE00 (E:-2-212)
1i: CATH_3c5yG00 (G:0-210)
1j: CATH_3c5yO00 (O:0-210)
1k: CATH_3c5yP00 (P:0-210)
1l: CATH_3c5yB00 (B:0-211)
1m: CATH_3c5yC00 (C:0-211)
1n: CATH_3c5yI00 (I:0-211)
1o: CATH_3c5yJ00 (J:0-211)
1p: CATH_3c5yK00 (K:0-211)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Ribose 5-phosphate Isomerase B; Chain: A,
(13)
Homologous Superfamily
:
[code=3.40.1400.10, no name defined]
(13)
Novosphingobium aromaticivorans dsm 12444. Organism_taxid: 279238. Strain: dsm 12444.
(1)
1a
3c5yA00
A:0-210
1b
3c5yD00
D:0-210
1c
3c5yM00
M:0-211
1d
3c5yN00
N:0-211
1e
3c5yF00
F:-1-211
1f
3c5yL00
L:0-212
1g
3c5yH00
H:-3-210
1h
3c5yE00
E:-2-212
1i
3c5yG00
G:0-210
1j
3c5yO00
O:0-210
1k
3c5yP00
P:0-210
1l
3c5yB00
B:0-211
1m
3c5yC00
C:0-211
1n
3c5yI00
I:0-211
1o
3c5yJ00
J:0-211
1p
3c5yK00
K:0-211
[
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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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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (611 KB)
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Biol.Unit 1 (154 KB)
Header - Biol.Unit 1
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