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4BEN
Asym. Unit
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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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
[
close entry info
]
Hetero Components
(5, 44)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
IM2
4
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
4
Ligand/Ion
MAGNESIUM ION
5
SO4
33
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(44, 44)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:282 , THR A:283 , HOH A:2076 , HOH A:2077 , HOH A:2177 , HOH A:2180
BINDING SITE FOR RESIDUE SO4 A1467
02
AC2
SOFTWARE
ALA A:234 , ARG A:236 , HOH A:2166
BINDING SITE FOR RESIDUE SO4 A1468
03
AC3
SOFTWARE
SER A:131 , ARG A:133 , LEU A:134
BINDING SITE FOR RESIDUE SO4 A1469
04
AC4
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161 , SO4 A:1476 , HOH A:2123 , HOH A:2129
BINDING SITE FOR RESIDUE SO4 A1470
05
AC5
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251
BINDING SITE FOR RESIDUE MG A 610
06
AC6
SOFTWARE
ALA A:402 , VAL A:406 , HIS A:462 , GLN A:463 , HOH A:2228
BINDING SITE FOR RESIDUE MG A 611
07
AC7
SOFTWARE
GLY A:268 , HOH A:2056
BINDING SITE FOR RESIDUE GOL A1471
08
AC8
SOFTWARE
ASP B:281 , HIS B:282 , THR B:283 , HOH B:2066
BINDING SITE FOR RESIDUE SO4 B1466
09
AC9
SOFTWARE
ALA B:234 , ARG B:236 , HOH B:2157 , HOH B:2220 , HOH B:2221
BINDING SITE FOR RESIDUE SO4 B1467
10
BC1
SOFTWARE
SER B:131 , ARG B:133 , LEU B:134
BINDING SITE FOR RESIDUE SO4 B1468
11
BC2
SOFTWARE
SO4 A:1475 , GLY B:159 , GLU B:160 , ARG B:161 , SO4 B:1472
BINDING SITE FOR RESIDUE SO4 B1469
12
BC3
SOFTWARE
HIS C:282 , THR C:283 , HOH C:2069 , HOH C:2070
BINDING SITE FOR RESIDUE SO4 C1466
13
BC4
SOFTWARE
ALA C:234 , ARG C:236 , HOH C:2166 , HOH C:2235
BINDING SITE FOR RESIDUE SO4 C1467
14
BC5
SOFTWARE
SER C:131 , GLU C:132 , ARG C:133 , LEU C:134 , HOH C:2236
BINDING SITE FOR RESIDUE SO4 C1468
15
BC6
SOFTWARE
GLY C:159 , GLU C:160 , ARG C:161 , SO4 C:1472 , HOH C:2117
BINDING SITE FOR RESIDUE SO4 C1469
16
BC7
SOFTWARE
HIS D:282 , THR D:283 , HOH D:2083 , HOH D:2084 , HOH D:2200
BINDING SITE FOR RESIDUE SO4 D1467
17
BC8
SOFTWARE
ARG D:236 , HOH D:2187
BINDING SITE FOR RESIDUE SO4 D1468
18
BC9
SOFTWARE
SER D:131 , ARG D:133 , LEU D:134 , HOH D:2267
BINDING SITE FOR RESIDUE SO4 D1469
19
CC1
SOFTWARE
GLY D:159 , GLU D:160 , ARG D:161 , SO4 D:1474 , HOH D:2139
BINDING SITE FOR RESIDUE SO4 D1470
20
CC2
SOFTWARE
GLU D:188 , HIS D:247 , GLU D:251
BINDING SITE FOR RESIDUE MG D 610
21
CC3
SOFTWARE
VAL D:406 , HIS D:462
BINDING SITE FOR RESIDUE MG D 611
22
CC4
SOFTWARE
GLY D:268
BINDING SITE FOR RESIDUE GOL D1471
23
CC5
SOFTWARE
HIS C:158 , GLY C:159 , SO4 C:1472
BINDING SITE FOR RESIDUE SO4 C1470
24
CC6
SOFTWARE
ASN D:195 , HOH D:2161 , HOH D:2166
BINDING SITE FOR RESIDUE SO4 D1472
25
CC7
SOFTWARE
SER B:38 , ARG B:39 , ASP B:40 , HOH B:2018
BINDING SITE FOR RESIDUE SO4 B1470
26
CC8
SOFTWARE
ASP A:130 , SER A:131
BINDING SITE FOR RESIDUE SO4 A1472
27
CC9
SOFTWARE
GLY A:70 , ARG A:93 , HOH A:2040
BINDING SITE FOR RESIDUE SO4 A1473
28
DC1
SOFTWARE
GLY D:70 , ARG D:93 , HOH D:2045
BINDING SITE FOR RESIDUE SO4 D1473
29
DC2
SOFTWARE
ARG A:39 , ASP A:40 , HOH A:2020
BINDING SITE FOR RESIDUE SO4 A1474
30
DC3
SOFTWARE
HIS B:158 , GLY B:159 , SO4 B:1472
BINDING SITE FOR RESIDUE SO4 B1471
31
DC4
SOFTWARE
SER A:204 , ALA A:205 , SO4 B:1469 , SO4 B:1472
BINDING SITE FOR RESIDUE SO4 A1475
32
DC5
SOFTWARE
ASP C:40 , HOH C:2020
BINDING SITE FOR RESIDUE SO4 C1471
33
DC6
SOFTWARE
HIS D:158 , GLU D:168 , SO4 D:1470 , HOH D:2152 , HOH D:2268
BINDING SITE FOR RESIDUE SO4 D1474
34
DC7
SOFTWARE
HIS A:158 , GLU A:168 , SO4 A:1470
BINDING SITE FOR RESIDUE SO4 A1476
35
DC8
SOFTWARE
GLY A:203 , SO4 A:1475 , HIS B:158 , GLU B:168 , LEU B:235 , SO4 B:1469 , SO4 B:1471
BINDING SITE FOR RESIDUE SO4 B1472
36
DC9
SOFTWARE
HIS C:158 , GLU C:168 , LEU C:235 , SO4 C:1469 , SO4 C:1470
BINDING SITE FOR RESIDUE SO4 C1472
37
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
38
EC2
SOFTWARE
HIS A:158 , GLY A:159 , HOH A:2066 , HOH A:2067
BINDING SITE FOR RESIDUE SO4 A1477
39
EC3
SOFTWARE
ALA A:229 , ALA A:230
BINDING SITE FOR RESIDUE SO4 A1478
40
EC4
SOFTWARE
TRP B:139 , SER B:415 , HOH B:2204
BINDING SITE FOR RESIDUE SO4 B1473
41
EC5
SOFTWARE
ALA A:48 , SER A:49 , SER A:298 , ASN A:300 , LEU A:349 , THR A:393 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , MET A:414 , HOH A:2241
BINDING SITE FOR LIGAND IM2 A 500 BOUND TO SER A 49
42
EC6
SOFTWARE
SER B:49 , SER B:298 , ASN B:300 , LEU B:349 , THR B:393 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , HOH B:2219
BINDING SITE FOR LIGAND IM2 B 500 BOUND TO SER B 49
43
EC7
SOFTWARE
SER C:49 , SER C:298 , ASN C:300 , LEU C:349 , THR C:393 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , HOH C:2218 , HOH C:2233
BINDING SITE FOR LIGAND IM2 C 500 BOUND TO SER C 49
44
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
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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_d4bena_ (A:)
1b: SCOP_d4benc_ (C:)
1c: SCOP_d4bend_ (D:)
1d: SCOP_d4benb_ (B:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
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:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (605 KB)
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