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4BEN
Biol. Unit 4
Info
Asym.Unit (605 KB)
Biol.Unit 1 (154 KB)
Biol.Unit 2 (152 KB)
Biol.Unit 3 (152 KB)
Biol.Unit 4 (154 KB)
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(1)
Title
:
R39-IMIPENEM ACYL-ENZYME CRYSTAL STRUCTURE
Authors
:
D. Van Elder, E. Sauvage, R. Herman, F. Kerff, M. Rocaboy, P. Charlier
Date
:
11 Mar 13 (Deposition) - 20 Mar 13 (Release) - 20 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
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
:
Hydrolase, Penicillin-Binding, Acyl-Enzyme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Sauvage, D. Van Elder, R. Herman, F. Kerff, R. F. Pratt, P. Charlier
Crystal Structures Of R39-Imipenem Acyl-Enzyme.
To Be Published
[
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: (5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXY... (IM2a)
2b: (5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXY... (IM2b)
2c: (5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXY... (IM2c)
2d: (5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXY... (IM2d)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
5a: SULFATE ION (SO4a)
5aa: SULFATE ION (SO4aa)
5ab: SULFATE ION (SO4ab)
5ac: SULFATE ION (SO4ac)
5ad: SULFATE ION (SO4ad)
5ae: SULFATE ION (SO4ae)
5af: SULFATE ION (SO4af)
5ag: SULFATE ION (SO4ag)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
5m: SULFATE ION (SO4m)
5n: SULFATE ION (SO4n)
5o: SULFATE ION (SO4o)
5p: SULFATE ION (SO4p)
5q: SULFATE ION (SO4q)
5r: SULFATE ION (SO4r)
5s: SULFATE ION (SO4s)
5t: SULFATE ION (SO4t)
5u: SULFATE ION (SO4u)
5v: SULFATE ION (SO4v)
5w: SULFATE ION (SO4w)
5x: SULFATE ION (SO4x)
5y: SULFATE ION (SO4y)
5z: SULFATE ION (SO4z)
View:
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Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
IM2
1
Ligand/Ion
(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
3
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
SO4
7
Ligand/Ion
SULFATE ION
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Sites
(12, 12)
Info
All Sites
01: BC7 (SOFTWARE)
02: BC8 (SOFTWARE)
03: BC9 (SOFTWARE)
04: CC1 (SOFTWARE)
05: CC2 (SOFTWARE)
06: CC3 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC6 (SOFTWARE)
09: DC1 (SOFTWARE)
10: DC6 (SOFTWARE)
11: EC1 (SOFTWARE)
12: EC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
BC7
SOFTWARE
HIS D:282 , THR D:283 , HOH D:2083 , HOH D:2084 , HOH D:2200
BINDING SITE FOR RESIDUE SO4 D1467
02
BC8
SOFTWARE
ARG D:236 , HOH D:2187
BINDING SITE FOR RESIDUE SO4 D1468
03
BC9
SOFTWARE
SER D:131 , ARG D:133 , LEU D:134 , HOH D:2267
BINDING SITE FOR RESIDUE SO4 D1469
04
CC1
SOFTWARE
GLY D:159 , GLU D:160 , ARG D:161 , SO4 D:1474 , HOH D:2139
BINDING SITE FOR RESIDUE SO4 D1470
05
CC2
SOFTWARE
GLU D:188 , HIS D:247 , GLU D:251
BINDING SITE FOR RESIDUE MG D 610
06
CC3
SOFTWARE
VAL D:406 , HIS D:462
BINDING SITE FOR RESIDUE MG D 611
07
CC4
SOFTWARE
GLY D:268
BINDING SITE FOR RESIDUE GOL D1471
08
CC6
SOFTWARE
ASN D:195 , HOH D:2161 , HOH D:2166
BINDING SITE FOR RESIDUE SO4 D1472
09
DC1
SOFTWARE
GLY D:70 , ARG D:93 , HOH D:2045
BINDING SITE FOR RESIDUE SO4 D1473
10
DC6
SOFTWARE
HIS D:158 , GLU D:168 , SO4 D:1470 , HOH D:2152 , HOH D:2268
BINDING SITE FOR RESIDUE SO4 D1474
11
EC1
SOFTWARE
GLY D:368 , GLN D:374 , TRP D:376 , SER D:377 , GLU D:408 , TYR D:423 , GLU D:430 , HOH D:2256
BINDING SITE FOR RESIDUE MES D1475
12
EC8
SOFTWARE
ALA D:48 , SER D:49 , SER D:298 , ASN D:300 , LEU D:349 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2033
BINDING SITE FOR LIGAND IM2 D 500 BOUND TO SER D 49
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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_d4bena_ (A:)
1b: SCOP_d4benc_ (C:)
1c: SCOP_d4bend_ (D:)
1d: SCOP_d4benb_ (B:)
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Protein Domains
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(
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Organisms
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)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta-lactamase/transpeptidase-like
(515)
Superfamily
:
beta-lactamase/transpeptidase-like
(515)
Family
:
Dac-like
(29)
Protein domain
:
D-alanyl-D-alanine carboxypeptidase Dac
(17)
Actinomadura sp. [TaxId: 1989]
(17)
1a
d4bena_
A:
1b
d4benc_
C:
1c
d4bend_
D:
1d
d4benb_
B:
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CATH Domains
(0, 0)
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Pfam Domains
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Chain D
Asymmetric Unit 1
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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'
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
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Show PDB file:
Asym.Unit (605 KB)
Header - Asym.Unit
Biol.Unit 1 (154 KB)
Header - Biol.Unit 1
Biol.Unit 2 (152 KB)
Header - Biol.Unit 2
Biol.Unit 3 (152 KB)
Header - Biol.Unit 3
Biol.Unit 4 (154 KB)
Header - Biol.Unit 4
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