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2GRU
Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (126 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 2-DEOXY-SCYLLO-INOSOSE SYNTHASE COMPLEXED WITH CARBAGLUCOSE-6-PHOSPHATE, NAD+ AND CO2+
Authors
:
E. Nango, T. Kumasaka
Date
:
25 Apr 06 (Deposition) - 08 May 07 (Release) - 29 Apr 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Aminoglycoside, 2-Deoxystreptamine, Dehydroquinate Synthase, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Nango, T. Kumasaka, T. Hirayama, N. Tanaka, T. Eguchi
Structure Of 2-Deoxy-Scyllo-Inosose Synthase, A Key Enzyme In The Biosynthesis Of 2-Deoxystreptamine-Containing Aminoglycoside Antibiotics, In Complex With A Mechanism-Based Inhibitor And Nad+
Proteins V. 70 517 2008
(for further references see the
PDB file header
)
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Hetero Components
(7, 11)
Info
All Hetero Components
1a: [(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYD... (CAKa)
2a: COBALT (II) ION (COa)
2b: COBALT (II) ION (COb)
3a: (1R,2S,3S,4R)-5-METHYLENECYCLOHEXA... (EXOa)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
4b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
6a: PHOSPHATE ION (PO4a)
7a: SULFITE ION (SO3a)
7b: SULFITE ION (SO3b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CAK
1
Ligand/Ion
[(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE
2
CO
2
Ligand/Ion
COBALT (II) ION
3
EXO
1
Ligand/Ion
(1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL
4
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
PO4
1
Ligand/Ion
PHOSPHATE ION
7
SO3
2
Ligand/Ion
SULFITE ION
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Sites
(11, 11)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:183 , HIS A:246 , HIS A:262 , EXO A:607 , HOH A:695
BINDING SITE FOR RESIDUE CO A 601
02
AC2
SOFTWARE
GLU A:243 , TYR A:244 , GLY A:245 , HIS A:246 , THR A:247 , ALA A:273 , MET A:335 , ILE A:336 , HOH A:721
BINDING SITE FOR RESIDUE SO3 A 605
03
AC3
SOFTWARE
LYS A:141 , ASN A:151 , LYS A:322 , EXO A:607 , ARG B:119
BINDING SITE FOR RESIDUE PO4 A 608
04
AC4
SOFTWARE
GLU B:183 , HIS B:246 , HIS B:262 , CAK B:609 , HOH B:701
BINDING SITE FOR RESIDUE CO B 602
05
AC5
SOFTWARE
GLU B:243 , TYR B:244 , GLY B:245 , HIS B:246 , THR B:247 , ALA B:273 , MET B:335 , ILE B:336 , HOH B:716
BINDING SITE FOR RESIDUE SO3 B 606
06
AC6
SOFTWARE
ASP A:42 , GLY A:44 , VAL A:45 , PRO A:46 , ILE A:49 , GLU A:72 , LYS A:75 , GLY A:103 , GLY A:104 , LEU A:105 , ASN A:108 , THR A:128 , THR A:129 , LEU A:131 , SER A:136 , SER A:139 , LYS A:141 , ASN A:151 , GLN A:176 , HOH A:669 , HOH A:696 , HOH A:708 , HOH A:728 , HOH A:751
BINDING SITE FOR RESIDUE NAD A 603
07
AC7
SOFTWARE
ASP A:135 , GLU A:183 , LYS A:186 , LYS A:225 , GLU A:235 , PHE A:242 , GLU A:243 , HIS A:246 , HIS A:262 , CO A:601 , PO4 A:608 , HOH A:616 , HOH A:695
BINDING SITE FOR RESIDUE EXO A 607
08
AC8
SOFTWARE
ARG A:119 , ASP B:42 , GLY B:44 , VAL B:45 , PRO B:46 , ILE B:49 , GLU B:72 , LYS B:75 , GLY B:103 , GLY B:104 , LEU B:105 , ASN B:108 , THR B:128 , THR B:129 , LEU B:131 , SER B:136 , LYS B:150 , ASN B:151 , GLN B:176 , CAK B:609 , HOH B:673 , HOH B:693 , HOH B:697 , HOH B:738 , HOH B:745
BINDING SITE FOR RESIDUE NAD B 604
09
AC9
SOFTWARE
ARG A:119 , ASP B:135 , LYS B:141 , ASN B:151 , GLU B:183 , LYS B:186 , LYS B:225 , GLU B:235 , PHE B:242 , HIS B:246 , HIS B:250 , HIS B:262 , CO B:602 , NAD B:604 , HOH B:635 , HOH B:701
BINDING SITE FOR RESIDUE CAK B 609
10
BC1
SOFTWARE
TYR A:52 , ARG A:167 , ILE A:168 , GLU A:171
BINDING SITE FOR RESIDUE MPD A 611
11
BC2
SOFTWARE
ASN B:278 , ASN B:281 , MET B:283
BINDING SITE FOR RESIDUE MPD B 610
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Asymmetric Unit 1
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