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3GXR
Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (35 KB)
Biol.Unit 2 (34 KB)
Biol.Unit 3 (32 KB)
Biol.Unit 4 (35 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF G-TYPE LYSOZYME FROM ATLANTIC COD (GADUS MORHUA L.) IN COMPLEX WITH NAG OLIGOMERS SHEDS NEW LIGHT ON SUBSTRATE BINDING AND THE CATALYTIC MECHANISM. STRUCTURE WITH NAG TO 1.7
Authors
:
R. Helland, R. L. Larsen, S. Finstad, P. Kyomuhendo, A. N. Larsen
Date
:
02 Apr 09 (Deposition) - 20 Oct 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Atlantic Cod, Fish Lysozyme, Active Site Residues, Substrate Binding Sites, Surface Potential, Muramidase Activity, Immune System, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Helland, R. L. Larsen, S. Finstad, P. Kyomuhendo, A. N. Larsen
Crystal Structures Of G-Type Lysozyme From Atlantic Cod She New Light On Substrate Binding And The Catalytic Mechanism.
Cell. Mol. Life Sci. V. 66 2585 2009
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Hetero Components
(1, 13)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
View:
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No.
Name
Count
Type
Full Name
1
NAG
13
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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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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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:105 , PHE A:127 , THR A:153 , GLY A:154 , ASP A:155 , GLY A:156 , ARG A:157 , NAG A:202
BINDING SITE FOR RESIDUE NAG A 201
02
AC2
SOFTWARE
GLN A:99 , ASP A:101 , TYR A:104 , HIS A:105 , PHE A:127 , TYR A:151 , THR A:153 , ARG A:157 , NAG A:201
BINDING SITE FOR RESIDUE NAG A 202
03
AC3
SOFTWARE
ARG A:72 , GLU A:73 , ILE A:80 , GLY A:89 , ASP A:90 , GLN A:99 , ASN A:152 , THR A:169 , HOH A:207 , HOH A:213 , HOH A:255 , NAG A:302
BINDING SITE FOR RESIDUE NAG A 301
04
AC4
SOFTWARE
GLN A:23 , ARG A:72 , GLU A:73 , HOH A:213 , HOH A:260 , HOH A:266 , NAG A:301 , NAG A:303
BINDING SITE FOR RESIDUE NAG A 302
05
AC5
SOFTWARE
ASP A:24 , ARG A:75 , ASN A:78 , VAL A:79 , HOH A:260 , NAG A:302
BINDING SITE FOR RESIDUE NAG A 303
06
AC6
SOFTWARE
ARG B:72 , GLU B:73 , VAL B:79 , ILE B:80 , GLY B:89 , ASP B:90 , GLN B:99 , ASN B:152 , THR B:169 , NAG B:302
BINDING SITE FOR RESIDUE NAG B 301
07
AC7
SOFTWARE
GLN B:23 , ARG B:72 , GLU B:73 , HOH B:220 , NAG B:301 , NAG B:303 , PRO D:136
BINDING SITE FOR RESIDUE NAG B 302
08
AC8
SOFTWARE
GLN B:23 , ASP B:24 , ARG B:75 , ASN B:78 , VAL B:79 , HOH B:213 , NAG B:302
BINDING SITE FOR RESIDUE NAG B 303
09
AC9
SOFTWARE
HIS D:105 , THR D:153 , GLY D:154 , ASP D:155 , GLY D:156 , ARG D:157 , NAG D:202 , HOH D:223
BINDING SITE FOR RESIDUE NAG D 201
10
BC1
SOFTWARE
ASP D:101 , HIS D:105 , PHE D:127 , TYR D:151 , ASN D:152 , THR D:153 , ARG D:157 , NAG D:201
BINDING SITE FOR RESIDUE NAG D 202
11
BC2
SOFTWARE
ARG D:72 , GLU D:73 , VAL D:79 , ILE D:80 , GLY D:89 , ASP D:90 , GLN D:99 , THR D:169 , HOH D:236 , NAG D:302
BINDING SITE FOR RESIDUE NAG D 301
12
BC3
SOFTWARE
GLN D:23 , ARG D:72 , GLU D:73 , ARG D:75 , NAG D:301 , NAG D:303
BINDING SITE FOR RESIDUE NAG D 302
13
BC4
SOFTWARE
GLN D:23 , ASP D:24 , ARG D:75 , ASN D:78 , VAL D:79 , NAG D:302
BINDING SITE FOR RESIDUE NAG D 303
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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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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3gxra_ (A:)
1b: SCOP_d3gxrb_ (B:)
1c: SCOP_d3gxrc_ (C:)
1d: SCOP_d3gxrd_ (D:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lysozyme-like
(1361)
Superfamily
:
Lysozyme-like
(1361)
Family
:
G-type lysozyme
(8)
Protein domain
:
automated matches
(4)
Atlantic cod (Gadus morhua) [TaxId: 8049]
(2)
1a
d3gxra_
A:
1b
d3gxrb_
B:
1c
d3gxrc_
C:
1d
d3gxrd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3gxrC00 (C:3-189)
1b: CATH_3gxrB00 (B:7-189)
1c: CATH_3gxrA00 (A:5-189)
1d: CATH_3gxrD00 (D:4-189)
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Organisms
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)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Lysozyme
(1131)
Homologous Superfamily
:
[code=1.10.530.10, no name defined]
(605)
Atlantic cod (Gadus morhua)
(2)
1a
3gxrC00
C:3-189
1b
3gxrB00
B:7-189
1c
3gxrA00
A:5-189
1d
3gxrD00
D:4-189
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Pfam Domains
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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
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (132 KB)
Header - Asym.Unit
Biol.Unit 1 (35 KB)
Header - Biol.Unit 1
Biol.Unit 2 (34 KB)
Header - Biol.Unit 2
Biol.Unit 3 (32 KB)
Header - Biol.Unit 3
Biol.Unit 4 (35 KB)
Header - Biol.Unit 4
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