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3FLU
Asym. Unit
Info
Asym.Unit (210 KB)
Biol.Unit 1 (203 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM THE PATHOGEN NEISSERIA MENINGITIDIS
Authors
:
S. R. A. Devenish, A. T. Hadfield
Date
:
19 Dec 08 (Deposition) - 23 Jun 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Tim Barrel, Beta-Alpha-Barrel, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. R. A. Devenish, F. H. A. Huisman, E. J. Parker, A. T. Hadfield, J. A. Gerrard
Cloning And Characterisation Of Dihydrodipicolinate Synthas From The Pathogen Neisseria Meningitidis.
Biochim. Biophys. Acta 2009
[
close entry info
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Hetero Components
(2, 47)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1aa: GLYCEROL (GOLaa)
1ab: GLYCEROL (GOLab)
1ac: GLYCEROL (GOLac)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
1t: GLYCEROL (GOLt)
1u: GLYCEROL (GOLu)
1v: GLYCEROL (GOLv)
1w: GLYCEROL (GOLw)
1x: GLYCEROL (GOLx)
1y: GLYCEROL (GOLy)
1z: GLYCEROL (GOLz)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
29
Ligand/Ion
GLYCEROL
2
SO4
18
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(47, 47)
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)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:80 , TYR A:106 , GOL A:298 , HOH A:309 , HOH A:452 , HOH A:891 , ASN B:80 , TYR B:106 , GOL B:297
BINDING SITE FOR RESIDUE SO4 A 292
02
AC2
SOFTWARE
TYR A:133 , ARG A:138 , GLY A:186 , PHE A:244 , SO4 A:294 , HOH A:384
BINDING SITE FOR RESIDUE SO4 A 293
03
AC3
SOFTWARE
ALA A:8 , GLY A:43 , THR A:44 , THR A:45 , LEU A:101 , TYR A:133 , LYS A:161 , ILE A:203 , SO4 A:293
BINDING SITE FOR RESIDUE SO4 A 294
04
AC4
SOFTWARE
LEU A:213 , ARG A:235 , GLN A:290 , HOH A:378
BINDING SITE FOR RESIDUE SO4 A 295
05
AC5
SOFTWARE
HIS A:189 , HOH A:415 , HOH A:873
BINDING SITE FOR RESIDUE SO4 A 296
06
AC6
SOFTWARE
ILE A:19 , HIS A:20 , TYR A:21 , GLU A:22 , ARG A:25 , HOH A:317
BINDING SITE FOR RESIDUE GOL A 297
07
AC7
SOFTWARE
SER A:48 , ALA A:49 , TYR A:106 , SO4 A:292 , HOH A:361 , HOH A:362 , HOH A:363 , HOH A:509 , ASN B:80 , TYR B:107
BINDING SITE FOR RESIDUE GOL A 298
08
AC8
SOFTWARE
TRP A:30 , ASN A:34 , PRO A:211 , LYS A:212 , HOH A:787 , HOH A:796
BINDING SITE FOR RESIDUE GOL A 299
09
AC9
SOFTWARE
SER A:257
BINDING SITE FOR RESIDUE GOL A 300
10
BC1
SOFTWARE
ASN A:14 , GLN A:15 , GLU A:263 , HIS A:265 , ASP C:29 , HIS C:66
BINDING SITE FOR RESIDUE GOL A 301
11
BC2
SOFTWARE
SER A:111 , GLN A:112 , HOH A:364 , HOH A:368 , HOH A:624
BINDING SITE FOR RESIDUE GOL A 302
12
BC3
SOFTWARE
THR A:144 , ASN A:145 , ASP A:146 , SER A:169 , HOH A:772
BINDING SITE FOR RESIDUE GOL A 303
13
BC4
SOFTWARE
MET B:1 , GLU B:179 , GLY B:180 , HIS B:200 , HOH B:398
BINDING SITE FOR RESIDUE SO4 B 292
14
BC5
SOFTWARE
ALA B:8 , GLY B:43 , THR B:44 , THR B:45 , LEU B:101 , TYR B:133 , LYS B:161 , ILE B:203 , SO4 B:295
BINDING SITE FOR RESIDUE SO4 B 293
15
BC6
SOFTWARE
HIS B:189 , HOH B:363
BINDING SITE FOR RESIDUE SO4 B 294
16
BC7
SOFTWARE
TYR B:133 , ARG B:138 , GLY B:186 , PHE B:244 , SO4 B:293
BINDING SITE FOR RESIDUE SO4 B 295
17
BC8
SOFTWARE
GLU A:275 , HOH A:645 , TRP B:254 , SER B:257 , ALA B:258 , PRO B:264
BINDING SITE FOR RESIDUE GOL B 296
18
BC9
SOFTWARE
ASN A:80 , TYR A:107 , SO4 A:292 , SER B:48 , ALA B:49 , TYR B:106 , HOH B:302 , HOH B:304 , HOH B:351 , HOH B:705
BINDING SITE FOR RESIDUE GOL B 297
19
CC1
SOFTWARE
ARG B:230 , GLU B:231 , ASP B:234 , HOH B:447 , ASN D:175
BINDING SITE FOR RESIDUE GOL B 298
20
CC2
SOFTWARE
LYS A:286 , HOH A:329 , TRP B:30 , ARG B:261 , HOH B:395 , HOH B:518 , HOH B:570
BINDING SITE FOR RESIDUE GOL B 299
21
CC3
SOFTWARE
SER B:111 , GLN B:112 , HOH B:357 , HOH B:358 , HOH B:614 , HOH B:644
BINDING SITE FOR RESIDUE GOL B 300
22
CC4
SOFTWARE
THR B:144 , ASN B:145 , ASP B:146 , SER B:169
BINDING SITE FOR RESIDUE GOL B 301
23
CC5
SOFTWARE
THR C:144 , ASN C:145 , SER C:169 , HOH C:330 , HOH C:352
BINDING SITE FOR RESIDUE SO4 C 292
24
CC6
SOFTWARE
ASN C:80 , TYR C:106 , GOL C:298 , HOH C:315 , ASN D:80 , TYR D:106 , GOL D:295 , HOH D:369
BINDING SITE FOR RESIDUE SO4 C 293
25
CC7
SOFTWARE
ALA C:8 , GLY C:43 , THR C:44 , THR C:45 , LEU C:101 , TYR C:133 , LYS C:161 , ILE C:203 , SO4 C:297 , GOL C:303
BINDING SITE FOR RESIDUE SO4 C 294
26
CC8
SOFTWARE
GLY C:180 , HIS C:200 , HOH C:367
BINDING SITE FOR RESIDUE SO4 C 295
27
CC9
SOFTWARE
HIS C:189 , PHE C:244 , HOH C:397 , HOH C:723
BINDING SITE FOR RESIDUE SO4 C 296
28
DC1
SOFTWARE
TYR C:133 , ARG C:138 , LYS C:161 , PHE C:244 , SO4 C:294 , HOH C:321
BINDING SITE FOR RESIDUE SO4 C 297
29
DC2
SOFTWARE
SER C:48 , ALA C:49 , GLY C:78 , TYR C:106 , SO4 C:293 , GOL C:303 , HOH C:946 , ASN D:80 , TYR D:107
BINDING SITE FOR RESIDUE GOL C 298
30
DC3
SOFTWARE
TRP C:254 , SER C:257
BINDING SITE FOR RESIDUE GOL C 299
31
DC4
SOFTWARE
GLU B:22 , ARG B:25 , HOH B:487 , ASN C:145 , ASP C:146 , LEU C:149 , GLU C:172
BINDING SITE FOR RESIDUE GOL C 300
32
DC5
SOFTWARE
THR C:274 , GLU C:275 , ASN C:276
BINDING SITE FOR RESIDUE GOL C 301
33
DC6
SOFTWARE
TRP C:30 , ASN C:34 , PRO C:211 , LYS C:212 , HOH C:362
BINDING SITE FOR RESIDUE GOL C 302
34
DC7
SOFTWARE
VAL C:42 , GLY C:43 , THR C:44 , SER C:48 , GLY C:76 , THR C:77 , GLY C:78 , LEU C:101 , SER C:102 , VAL C:103 , SO4 C:294 , GOL C:298 , HOH C:358 , TYR D:107
BINDING SITE FOR RESIDUE GOL C 303
35
DC8
SOFTWARE
LYS C:109 , SO4 D:292 , SO4 D:294 , HOH D:379
BINDING SITE FOR RESIDUE GOL C 304
36
DC9
SOFTWARE
SER C:111 , GLN C:112 , HOH C:369 , HOH C:603 , HOH C:765
BINDING SITE FOR RESIDUE GOL C 305
37
EC1
SOFTWARE
GOL C:304 , TYR D:133 , VAL D:135 , ARG D:138 , ALA D:163 , GLY D:186 , PHE D:244 , SO4 D:293
BINDING SITE FOR RESIDUE SO4 D 292
38
EC2
SOFTWARE
ALA D:8 , GLY D:43 , THR D:44 , THR D:45 , LEU D:101 , TYR D:133 , LYS D:161 , ILE D:203 , SO4 D:292 , GOL D:296
BINDING SITE FOR RESIDUE SO4 D 293
39
EC3
SOFTWARE
GOL C:304 , HIS D:189 , HOH D:322 , HOH D:872
BINDING SITE FOR RESIDUE SO4 D 294
40
EC4
SOFTWARE
ASN C:80 , SO4 C:293 , SER D:48 , ALA D:49 , GLY D:78 , TYR D:106 , GOL D:296 , HOH D:685 , HOH D:943
BINDING SITE FOR RESIDUE GOL D 295
41
EC5
SOFTWARE
TYR C:107 , VAL D:42 , GLY D:43 , THR D:44 , SER D:48 , GLY D:76 , THR D:77 , GLY D:78 , LEU D:101 , SER D:102 , VAL D:103 , SO4 D:293 , GOL D:295 , HOH D:685
BINDING SITE FOR RESIDUE GOL D 296
42
EC6
SOFTWARE
HIS D:20 , TYR D:21 , GLU D:22 , ARG D:25 , HOH D:629
BINDING SITE FOR RESIDUE GOL D 297
43
EC7
SOFTWARE
HIS B:189 , ASP B:241 , HOH B:392 , ASN D:166 , GLY D:168 , SER D:169 , GLU D:172
BINDING SITE FOR RESIDUE GOL D 298
44
EC8
SOFTWARE
GLN A:90 , TRP D:254 , SER D:257 , PRO D:264 , HOH D:648
BINDING SITE FOR RESIDUE GOL D 299
45
EC9
SOFTWARE
ASN D:14 , GLN D:15 , GLU D:263 , HIS D:265 , HOH D:802
BINDING SITE FOR RESIDUE GOL D 300
46
FC1
SOFTWARE
THR D:144 , ASN D:145 , ASP D:146 , SER D:169
BINDING SITE FOR RESIDUE GOL D 301
47
FC2
SOFTWARE
SER D:111 , GLN D:112 , HOH D:331 , HOH D:364 , HOH D:686 , HOH D:747
BINDING SITE FOR RESIDUE GOL D 302
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DHDPS_1 (A:38-55,B:38-55,C:38-55,D:38-55)
2: DHDPS_2 (A:133-163,B:133-163,C:133-163,D:13...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHDPS_1
PS00665
Dihydrodipicolinate synthase signature 1.
DAPA_NEIMB
38-55
4
A:38-55
B:38-55
C:38-55
D:38-55
2
DHDPS_2
PS00666
Dihydrodipicolinate synthase signature 2.
DAPA_NEIMB
133-163
4
A:133-163
B:133-163
C:133-163
D:133-163
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
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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_d3flua_ (A:)
1b: SCOP_d3flub_ (B:)
1c: SCOP_d3fluc_ (C:)
1d: SCOP_d3flud_ (D:)
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Folds
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Superfamilies
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Families
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
automated matches
(113)
Protein domain
:
automated matches
(113)
Neisseria meningitidis [TaxId: 491]
(1)
1a
d3flua_
A:
1b
d3flub_
B:
1c
d3fluc_
C:
1d
d3flud_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3fluB00 (B:1-291)
1b: CATH_3fluC00 (C:0-291)
1c: CATH_3fluD00 (D:-1-291)
1d: CATH_3fluA00 (A:-2-291)
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Neisseria meningitidis serogroup b. Organism_taxid: 491. Strain: serogroup b.
(1)
1a
3fluB00
B:1-291
1b
3fluC00
C:0-291
1c
3fluD00
D:-1-291
1d
3fluA00
A:-2-291
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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