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4B4Z
Asym. Unit
Info
Asym.Unit (301 KB)
Biol.Unit 1 (79 KB)
Biol.Unit 2 (78 KB)
Biol.Unit 3 (79 KB)
Biol.Unit 4 (76 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A SULFONAMIDE BORONATE INHIBITOR
Authors
:
S. E. Cannella, E. Sauvage, R. Herman, F. Kerff, M. Rocaboy, P. Charlier
Date
:
02 Aug 12 (Deposition) - 21 Aug 13 (Release) - 21 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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, Boronic Acid, Peptidoglycan
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Sauvage
Crystal Structure Of A Complex Between Actinomadura R39 Dd-Peptidase And A Boronate Inhibitor
To Be Published
[
close entry info
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Hetero Components
(3, 34)
Info
All Hetero Components
1a: {[(BENZYLSULFONYL)AMINO]METHYL}BOR... (BSFa)
1b: {[(BENZYLSULFONYL)AMINO]METHYL}BOR... (BSFb)
1c: {[(BENZYLSULFONYL)AMINO]METHYL}BOR... (BSFc)
1d: {[(BENZYLSULFONYL)AMINO]METHYL}BOR... (BSFd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
3x: SULFATE ION (SO4x)
3y: SULFATE ION (SO4y)
3z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BSF
4
Ligand/Ion
{[(BENZYLSULFONYL)AMINO]METHYL}BORONIC ACID
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
SO4
26
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(34, 34)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:49 , LYS A:52 , PHE A:297 , SER A:298 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , HOH A:2028 , ALA B:175
BINDING SITE FOR RESIDUE BSF A 500
02
AC2
SOFTWARE
HIS A:282 , THR A:283 , HOH A:2209 , HOH A:2210
BINDING SITE FOR RESIDUE SO4 A1467
03
AC3
SOFTWARE
ALA A:234 , ARG A:236 , HOH A:2278
BINDING SITE FOR RESIDUE SO4 A1468
04
AC4
SOFTWARE
SER A:131 , ARG A:133 , LEU A:134
BINDING SITE FOR RESIDUE SO4 A1469
05
AC5
SOFTWARE
GLY A:159 , GLU A:160 , ARG A:161 , SO4 A:1473 , HOH A:2133 , HOH A:2280
BINDING SITE FOR RESIDUE SO4 A1470
06
AC6
SOFTWARE
GLU A:188 , HIS A:247 , GLU A:251
BINDING SITE FOR RESIDUE MG A 610
07
AC7
SOFTWARE
GLU A:404
BINDING SITE FOR RESIDUE MG A 611
08
AC8
SOFTWARE
SER B:49 , LYS B:52 , SER B:298 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , HOH B:2204 , HOH B:2206
BINDING SITE FOR RESIDUE BSF B 500
09
AC9
SOFTWARE
HIS B:282 , THR B:283
BINDING SITE FOR RESIDUE SO4 B1466
10
BC1
SOFTWARE
ALA B:234 , ARG B:236 , HOH B:2180 , HOH B:2271 , HOH B:2272
BINDING SITE FOR RESIDUE SO4 B1467
11
BC2
SOFTWARE
SER B:131 , ARG B:133 , LEU B:134
BINDING SITE FOR RESIDUE SO4 B1468
12
BC3
SOFTWARE
GLY B:159 , GLU B:160 , ARG B:161 , SO4 B:1472 , HOH B:2131
BINDING SITE FOR RESIDUE SO4 B1469
13
BC4
SOFTWARE
SER C:49 , PHE C:297 , SER C:298 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , HOH C:2229 , HOH C:2276
BINDING SITE FOR RESIDUE BSF C 500
14
BC5
SOFTWARE
HIS C:282 , THR C:283 , HOH C:2087
BINDING SITE FOR RESIDUE SO4 C1466
15
BC6
SOFTWARE
ARG C:236 , HOH C:2294
BINDING SITE FOR RESIDUE SO4 C1467
16
BC7
SOFTWARE
SER C:131 , GLU C:132 , ARG C:133 , LEU C:134 , HOH C:2103
BINDING SITE FOR RESIDUE SO4 C1468
17
BC8
SOFTWARE
GLY C:159 , GLU C:160 , ARG C:161 , SO4 C:1472 , HOH C:2145
BINDING SITE FOR RESIDUE SO4 C1469
18
BC9
SOFTWARE
SER D:49 , LYS D:52 , SER D:298 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2016 , HOH D:2187
BINDING SITE FOR RESIDUE BSF D 500
19
CC1
SOFTWARE
ASP D:281 , HIS D:282 , THR D:283 , HOH D:2053
BINDING SITE FOR RESIDUE SO4 D1467
20
CC2
SOFTWARE
ALA D:234 , ARG D:236 , HOH D:2199
BINDING SITE FOR RESIDUE SO4 D1468
21
CC3
SOFTWARE
SER D:131 , ARG D:133 , LEU D:134 , HOH D:2201 , HOH D:2202 , HOH D:2203
BINDING SITE FOR RESIDUE SO4 D1469
22
CC4
SOFTWARE
GLY D:159 , GLU D:160 , ARG D:161 , SO4 D:1471 , HOH D:2106
BINDING SITE FOR RESIDUE SO4 D1470
23
CC5
SOFTWARE
GLU D:188 , HIS D:247 , GLU D:251
BINDING SITE FOR RESIDUE MG D 610
24
CC6
SOFTWARE
VAL D:406 , HIS D:462
BINDING SITE FOR RESIDUE MG D 611
25
CC7
SOFTWARE
HIS C:158 , GLY C:159 , SO4 C:1472 , HOH C:2082
BINDING SITE FOR RESIDUE SO4 C1470
26
CC8
SOFTWARE
ARG A:39 , ASP A:40 , HOH A:2023
BINDING SITE FOR RESIDUE SO4 A1471
27
CC9
SOFTWARE
GLU A:192 , LEU A:193 , HOH A:2156
BINDING SITE FOR RESIDUE SO4 A1472
28
DC1
SOFTWARE
ARG B:39 , ASP B:40
BINDING SITE FOR RESIDUE SO4 B1470
29
DC2
SOFTWARE
TRP B:139 , SER B:415 , HOH B:2257
BINDING SITE FOR RESIDUE SO4 B1471
30
DC3
SOFTWARE
THR C:413 , HOH C:2122 , HOH C:2134
BINDING SITE FOR RESIDUE SO4 C1471
31
DC4
SOFTWARE
GLY A:203 , HIS B:158 , GLU B:168 , LEU B:235 , SO4 B:1469
BINDING SITE FOR RESIDUE SO4 B1472
32
DC5
SOFTWARE
HIS C:158 , GLU C:168 , SO4 C:1469 , SO4 C:1470
BINDING SITE FOR RESIDUE SO4 C1472
33
DC6
SOFTWARE
HIS D:158 , GLU D:168 , SO4 D:1470 , HOH D:2104
BINDING SITE FOR RESIDUE SO4 D1471
34
DC7
SOFTWARE
HIS A:158 , GLU A:168 , SO4 A:1470 , HOH A:2146 , HOH A:2279 , HOH A:2280
BINDING SITE FOR RESIDUE SO4 A1473
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d4b4za_ (A:)
1b: SCOP_d4b4zb_ (B:)
1c: SCOP_d4b4zc_ (C:)
1d: SCOP_d4b4zd_ (D:)
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Protein Domains
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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
d4b4za_
A:
1b
d4b4zb_
B:
1c
d4b4zc_
C:
1d
d4b4zd_
D:
[
close SCOP info
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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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