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3ZDV
Biol. Unit 1
Info
Asym.Unit (169 KB)
Biol.Unit 1 (162 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH METHYL 6-(2,4,6-TRIMETHYLPHENYLSULFONYLAMIDO)-6-DEOXY-ALPHA-D-MANNOPYRANOSIDE
Authors
:
D. Hauck, I. Joachim, B. Frommeyer, A. Varrot, B. Philipp, H. M. Moller, A. Imberty, T. E. Exner, A. Titz
Date
:
30 Nov 12 (Deposition) - 18 Sep 13 (Release) - 13 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.41
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Sugar Binding Protein, Glycomimetic, Inhibitor
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
D. Hauck, I. Joachim, B. Frommeyer, A. Varrot, B. Philipp, H. M. Moller A. Imberty, T. E. Exner, A. Titz
Discovery Of Two Classes Of Potent Glycomimetic Inhibitors Of Pseudomonas Aeruginosa Lecb With Distinct Binding Modes.
Acs Chem. Biol. V. 8 1775 2013
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Hetero Components
(5, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: 1,2-ETHANEDIOL (EDOa)
3a: 2,4,6-TRIMETHYLBENZENESULFONAMIDE (F1Aa)
3b: 2,4,6-TRIMETHYLBENZENESULFONAMIDE (F1Ab)
3c: 2,4,6-TRIMETHYLBENZENESULFONAMIDE (F1Ac)
3d: 2,4,6-TRIMETHYLBENZENESULFONAMIDE (F1Ad)
4a: GLYCEROL (GOLa)
5a: O1-METHYL-MANNOSE (MMAa)
5b: O1-METHYL-MANNOSE (MMAb)
5c: O1-METHYL-MANNOSE (MMAc)
5d: O1-METHYL-MANNOSE (MMAd)
6a: SULFATE ION (SO4a)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
3
F1A
4
Ligand/Ion
2,4,6-TRIMETHYLBENZENESULFONAMIDE
4
GOL
1
Ligand/Ion
GLYCEROL
5
MMA
4
Ligand/Ion
O1-METHYL-MANNOSE
6
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(15, 15)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:95 , ASP A:99 , ASP A:101 , ASP A:104 , MMA A:201
BINDING SITE FOR RESIDUE CA A 199
02
AC2
SOFTWARE
ASN A:21 , ASP A:101 , ASN A:103 , ASP A:104 , MMA A:201 , GLY B:114
BINDING SITE FOR RESIDUE CA A 200
03
AC3
SOFTWARE
GLU B:95 , ASP B:99 , ASP B:101 , ASP B:104 , MMA B:201
BINDING SITE FOR RESIDUE CA B 199
04
AC4
SOFTWARE
GLY A:114 , ASN B:21 , ASP B:101 , ASN B:103 , ASP B:104 , MMA B:201
BINDING SITE FOR RESIDUE CA B 200
05
AC5
SOFTWARE
GLU C:95 , ASP C:99 , ASP C:101 , ASP C:104 , MMA C:201
BINDING SITE FOR RESIDUE CA C 199
06
AC6
SOFTWARE
ASN C:21 , ASP C:101 , ASN C:103 , ASP C:104 , MMA C:201 , GLY D:114
BINDING SITE FOR RESIDUE CA C 200
07
AC7
SOFTWARE
GLU D:95 , ASP D:99 , ASP D:101 , ASP D:104 , MMA D:201
BINDING SITE FOR RESIDUE CA D 199
08
AC8
SOFTWARE
GLY C:114 , ASN D:21 , ASP D:101 , ASN D:103 , ASP D:104 , MMA D:201
BINDING SITE FOR RESIDUE CA D 200
09
AC9
SOFTWARE
GLN B:53 , VAL B:54 , HOH B:2057 , HOH B:2069 , HOH B:2116 , ALA D:38 , THR D:39 , GLN D:53
BINDING SITE FOR RESIDUE GOL B 203
10
BC1
SOFTWARE
SER B:44 , ASN B:46 , ALA B:48 , HOH B:2065 , SER D:44 , THR D:45 , ASN D:46 , HOH D:2050 , HOH D:2053 , HOH D:2092
BINDING SITE FOR RESIDUE SO4 D 204
11
BC2
SOFTWARE
ALA B:1 , HOH B:2117 , HOH B:2118 , ALA D:1
BINDING SITE FOR RESIDUE EDO B1115
12
BC3
SOFTWARE
ARG A:13 , ASN A:21 , SER A:22 , SER A:23 , GLU A:95 , ASP A:96 , ASP A:99 , ASP A:101 , ASP A:104 , GLY A:114 , CA A:199 , CA A:200 , HOH A:2127 , HOH A:2134 , SER B:23 , THR B:45 , GLY B:114 , MMA B:201
BINDING SITE FOR RESIDUES MMA A 201 AND F1A A 202
13
BC4
SOFTWARE
GLY A:114 , F1A A:202 , ASN B:21 , SER B:22 , SER B:23 , GLY B:24 , GLU B:95 , ASP B:96 , ASP B:99 , ASP B:101 , ASP B:104 , CA B:199 , CA B:200 , HOH B:2105
BINDING SITE FOR RESIDUES MMA B 201 AND F1A B 202
14
BC5
SOFTWARE
ASN C:21 , SER C:22 , SER C:23 , GLU C:95 , ASP C:96 , ASP C:99 , ASP C:101 , ASP C:104 , CA C:199 , CA C:200 , HOH C:2100 , HOH C:2109 , ASN D:70 , GLY D:114 , F1A D:202 , HOH D:2084
BINDING SITE FOR RESIDUES MMA C 201 AND F1A C 202
15
BC6
SOFTWARE
ARG C:72 , GLY C:114 , F1A C:202 , ASN D:21 , SER D:22 , SER D:23 , GLU D:95 , ASP D:96 , ASP D:99 , ASP D:101 , ASP D:104 , CA D:199 , CA D:200 , HOH D:2086 , HOH D:2091
BINDING SITE FOR RESIDUES MMA D 201 AND F1A D 202
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3zdva_ (A:)
1b: SCOP_d3zdvb_ (B:)
1c: SCOP_d3zdvc_ (C:)
1d: SCOP_d3zdvd_ (D:)
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Class
:
All beta proteins
(24004)
Fold
:
Calcium-mediated lectin
(32)
Superfamily
:
Calcium-mediated lectin
(32)
Family
:
Calcium-mediated lectin
(25)
Protein domain
:
Fucose-binding lectin II (PA-LII)
(9)
Pseudomonas aeruginosa [TaxId: 287]
(9)
1a
d3zdva_
A:
1b
d3zdvb_
B:
1c
d3zdvc_
C:
1d
d3zdvd_
D:
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CATH Domains
(0, 0)
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Pfam Domains
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Chain A
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Chain D
Asymmetric Unit 1
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Example Command
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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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Asym.Unit (169 KB)
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