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1X7D
Asym. Unit
Info
Asym.Unit (134 KB)
Biol.Unit 1 (127 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF ORNITHINE CYCLODEAMINASE COMPLEXED WITH NAD AND ORNITHINE TO 1.6 ANGSTROMS
Authors
:
S. Alam, J. L. Goodman, S. Wang, F. J. Ruzicka, P. A. Frey, J. E. Wedekind
Date
:
13 Aug 04 (Deposition) - 09 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Deaminase, Binds Nad+, Binds L-Ornithine, Binds L-Proline, 2 Helix Bundle, Beta Barrel, Rossmann Fold, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Goodman, S. Wang, S. Alam, F. J. Ruzicka, P. A. Frey, J. E. Wedekind
Ornithine Cyclodeaminase: Structure, Mechanism Of Action, And Implications For The U-Crystallin Family
Biochemistry V. 43 13883 2004
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Hetero Components
(6, 29)
Info
All Hetero Components
1a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
2f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
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)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
6a: L-ORNITHINE (ORNa)
6b: L-ORNITHINE (ORNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2
MPD
6
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
4
NA
2
Ligand/Ion
SODIUM ION
5
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
ORN
2
Ligand/Ion
L-ORNITHINE
[
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Sites
(13, 13)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:224 , VAL A:225 , GLY A:227 , SER A:293 , HOH A:1513 , HOH A:1879
BINDING SITE FOR RESIDUE NA A 1501
02
AC2
SOFTWARE
ALA B:224 , VAL B:225 , GLY B:227 , SER B:293 , HOH B:3176 , HOH B:3315
BINDING SITE FOR RESIDUE NA B 1502
03
AC3
SOFTWARE
LYS A:331 , ORN A:1102 , HOH A:1516 , HOH A:1668 , THR B:84 , ARG B:112 , THR B:113 , GLY B:138 , ALA B:139 , GLN B:140 , ASP B:161 , THR B:162 , VAL B:201 , THR B:202 , ALA B:203 , ILE B:210 , VAL B:225 , GLY B:226 , ASP B:228 , LYS B:232 , SER B:293 , VAL B:294 , GLY B:295 , HOH B:3165 , HOH B:3166 , HOH B:3170 , HOH B:3209 , HOH B:3223 , HOH B:3323 , HOH B:3387 , HOH B:3538
BINDING SITE FOR RESIDUE NAD B 1301
04
AC4
SOFTWARE
THR A:84 , ARG A:112 , THR A:113 , GLY A:138 , ALA A:139 , GLN A:140 , ASP A:161 , THR A:162 , VAL A:201 , THR A:202 , ALA A:203 , ILE A:210 , VAL A:225 , GLY A:226 , ASP A:228 , LYS A:232 , SER A:293 , VAL A:294 , GLY A:295 , ORN A:1101 , HOH A:1503 , HOH A:1504 , HOH A:1512 , HOH A:1519 , HOH A:1559 , HOH A:1598 , HOH A:1610 , HOH A:1686 , HOH A:1695 , HOH A:1801 , LYS B:331
BINDING SITE FOR RESIDUE NAD A 1302
05
AC5
SOFTWARE
ARG A:45 , VAL A:54 , GLU A:56 , LYS A:69 , VAL A:71 , ASN A:72 , GLY A:73 , VAL A:85 , ARG A:112 , ASP A:228 , VAL A:294 , GLY A:295 , NAD A:1302 , HOH A:1558 , HOH A:1642 , HOH A:1695
BINDING SITE FOR RESIDUE ORN A 1101
06
AC6
SOFTWARE
HOH A:1611 , ARG B:45 , VAL B:54 , GLU B:56 , MSE B:58 , LYS B:69 , ASN B:72 , GLY B:73 , VAL B:85 , ARG B:112 , ASP B:228 , VAL B:294 , GLY B:295 , NAD B:1301 , HOH B:3207
BINDING SITE FOR RESIDUE ORN A 1102
07
AC7
SOFTWARE
GLN A:283 , SER A:284 , GLN A:287 , ARG A:338 , HOH A:1793 , HIS B:15 , GLU B:176 , TYR B:177 , HOH B:3259
BINDING SITE FOR RESIDUE MES B 3158
08
AC8
SOFTWARE
GLN A:38 , ALA A:39 , PHE A:40 , ASP A:62 , LYS A:63 , MPD A:1402
BINDING SITE FOR RESIDUE MPD A 1401
09
AC9
SOFTWARE
GLN A:38 , ALA A:39 , MPD A:1401 , LEU B:216 , ASN B:242 , SER B:286 , HOH B:3440
BINDING SITE FOR RESIDUE MPD A 1402
10
BC1
SOFTWARE
SER A:64 , ARG A:65 , LEU A:91 , ASP A:93 , VAL A:100 , HOH A:1592
BINDING SITE FOR RESIDUE MPD A 1403
11
BC2
SOFTWARE
TYR A:3 , ALA A:311 , GLU A:312 , MSE A:316
BINDING SITE FOR RESIDUE MPD A 1404
12
BC3
SOFTWARE
TYR B:3 , ALA B:311 , GLU B:312 , GLY B:315 , MSE B:316
BINDING SITE FOR RESIDUE MPD B 1405
13
BC4
SOFTWARE
SER B:64 , ARG B:65 , ALA B:92 , ASP B:93 , VAL B:100 , LEU B:308 , HOH B:3267 , HOH B:3513
BINDING SITE FOR RESIDUE MPD B 1406
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1x7da_ (A:)
1b: SCOP_d1x7db_ (B:)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Ornithine cyclodeaminase-like
(4)
Protein domain
:
Ornithine cyclodeaminase
(2)
Pseudomonas putida [TaxId: 303]
(2)
1a
d1x7da_
A:
1b
d1x7db_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1x7dA01 (A:2-125,A:296-341)
1b: CATH_1x7dB01 (B:2-125,B:296-340)
2a: CATH_1x7dA02 (A:126-295)
2b: CATH_1x7dB02 (B:126-295)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
ornithine cyclodeaminase, domain 1
(2)
Homologous Superfamily
:
ornithine cyclodeaminase, domain 1
(2)
Pseudomonas putida. Organism_taxid: 303.
(2)
1a
1x7dA01
A:2-125,A:296-341
1b
1x7dB01
B:2-125,B:296-340
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pseudomonas putida. Organism_taxid: 303.
(5)
2a
1x7dA02
A:126-295
2b
1x7dB02
B:126-295
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_OCD_Mu_crystall_1x7dB01 (B:7-315)
1b: PFAM_OCD_Mu_crystall_1x7dB02 (B:7-315)
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)
Clan
:
NADP_Rossmann
(1239)
Family
:
OCD_Mu_crystall
(2)
Pseudomonas putida (strain KT2440)
(2)
1a
OCD_Mu_crystall-1x7dB01
B:7-315
1b
OCD_Mu_crystall-1x7dB02
B:7-315
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Asymmetric Unit 1
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