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4LVC
Asym. Unit
Info
Asym.Unit (674 KB)
Biol.Unit 1 (665 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE FROM BRADYRHIZOBIUM ELKANII IN COMPLEX WITH ADENOSINE
Authors
:
T. Manszewski, K. Singh, B. Imiolczyk, M. Jaskolski
Date
:
26 Jul 13 (Deposition) - 30 Jul 14 (Release) - 16 Dec 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.74
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Cellular Methylation, Sah Hydrolysis, Nad+ Cofactor, Atmospheric Nitrogen Fixation, Rhizobium-Legume Symbiosis, Hydrolase, Nad+ Cofactor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Manszewski, K. Singh, B. Imiolczyk, M. Jaskolski
An Enzyme Captured In Two Conformational States: Crystal Structure Of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii.
Acta Crystallogr. , Sect. D V. 71 2422 2015
(for further references see the
PDB file header
)
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Hetero Components
(5, 28)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
2a: ADENOSINE (ADNa)
2b: ADENOSINE (ADNb)
2c: ADENOSINE (ADNc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
4d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
5a: AMMONIUM ION (NH4a)
5b: AMMONIUM ION (NH4b)
5c: AMMONIUM ION (NH4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
ADN
3
Ligand/Ion
ADENOSINE
3
GOL
15
Ligand/Ion
GLYCEROL
4
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
5
NH4
3
Ligand/Ion
AMMONIUM ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:57 , HIS A:58 , THR A:60 , GLN A:62 , THR A:63 , ASP A:135 , GLU A:197 , THR A:198 , LYS A:227 , ASP A:231 , HIS A:342 , LEU A:383 , MET A:390 , GLY A:391 , HIS A:392 , MET A:397 , PHE A:401 , NAD A:503
BINDING SITE FOR RESIDUE ADN A 501
02
AC2
SOFTWARE
GLN A:62 , MET A:390 , HIS A:392 , HOH A:717 , HOH A:763 , HOH C:620
BINDING SITE FOR RESIDUE NH4 A 502
03
AC3
SOFTWARE
THR A:198 , THR A:199 , THR A:200 , ASN A:232 , GLY A:263 , ASP A:264 , VAL A:265 , GLU A:284 , VAL A:285 , ASP A:286 , CYS A:289 , THR A:317 , GLY A:318 , ASN A:319 , ILE A:322 , ILE A:340 , GLY A:341 , HIS A:342 , LEU A:383 , ASN A:385 , HIS A:392 , ADN A:501 , HOH A:604 , HOH A:626 , HOH A:641 , HOH A:719 , HOH A:787 , HOH A:813 , GLN B:454 , LYS B:467 , TYR B:471
BINDING SITE FOR RESIDUE NAD A 503
04
AC4
SOFTWARE
THR A:200 , HIS A:203 , GLY A:318 , HOH A:786 , HOH A:1009 , TYR B:457
BINDING SITE FOR RESIDUE GOL A 504
05
AC5
SOFTWARE
LEU A:427 , LYS A:429 , ASP A:432 , ASP A:469 , ARG B:472
BINDING SITE FOR RESIDUE GOL A 505
06
AC6
SOFTWARE
LYS A:106 , ARG A:246 , GLY A:387 , ASN A:388 , ALA A:389 , HOH A:1026
BINDING SITE FOR RESIDUE GOL A 506
07
AC7
SOFTWARE
HIS B:58 , THR B:60 , GLN B:62 , THR B:63 , ASP B:135 , GLU B:197 , THR B:198 , LYS B:227 , ASP B:231 , HIS B:342 , MET B:390 , GLY B:391 , HIS B:392 , MET B:397 , PHE B:401 , NAD B:503
BINDING SITE FOR RESIDUE ADN B 501
08
AC8
SOFTWARE
GLN B:62 , MET B:390 , HIS B:392 , HOH B:635 , HOH B:756 , HOH D:630
BINDING SITE FOR RESIDUE NH4 B 502
09
AC9
SOFTWARE
GLN A:454 , LYS A:467 , TYR A:471 , THR B:198 , THR B:199 , THR B:200 , ASN B:232 , GLY B:261 , GLY B:263 , ASP B:264 , VAL B:265 , SER B:283 , GLU B:284 , VAL B:285 , ASP B:286 , CYS B:289 , THR B:317 , GLY B:318 , ASN B:319 , ILE B:322 , ILE B:340 , GLY B:341 , HIS B:342 , ASN B:385 , HIS B:392 , ADN B:501 , HOH B:628 , HOH B:631 , HOH B:644 , HOH B:713 , HOH B:735 , HOH B:741
BINDING SITE FOR RESIDUE NAD B 503
10
BC1
SOFTWARE
ARG A:472 , VAL B:426 , LEU B:427 , LYS B:429 , ASP B:432 , ASP B:469
BINDING SITE FOR RESIDUE GOL B 504
11
BC2
SOFTWARE
LYS A:452 , ASP A:453 , PRO B:33 , GLU B:40 , HOH B:679 , HOH B:697 , HOH B:761
BINDING SITE FOR RESIDUE GOL B 505
12
BC3
SOFTWARE
LYS B:106 , ARG B:246 , GLY B:387 , ASN B:388 , ALA B:389 , HOH B:645 , HOH B:690 , HOH B:819
BINDING SITE FOR RESIDUE GOL B 506
13
BC4
SOFTWARE
GLY B:254 , ARG B:279 , ALA C:294 , TYR C:298 , GLU C:299 , VAL C:300 , ILE D:443 , GLY D:444
BINDING SITE FOR RESIDUE GOL B 507
14
BC5
SOFTWARE
LYS B:106 , GLN B:363
BINDING SITE FOR RESIDUE ACT B 508
15
BC6
SOFTWARE
GLY B:459
BINDING SITE FOR RESIDUE ACT B 509
16
BC7
SOFTWARE
HIS C:58 , THR C:60 , GLN C:62 , THR C:63 , ASP C:135 , GLU C:197 , THR C:198 , LYS C:227 , ASP C:231 , HIS C:342 , MET C:390 , HIS C:392 , MET C:397 , PHE C:401 , NAD C:503
BINDING SITE FOR RESIDUE ADN C 501
17
BC8
SOFTWARE
HOH A:663 , GLN C:62 , MET C:390 , HIS C:392 , HOH C:676 , HOH C:722
BINDING SITE FOR RESIDUE NH4 C 502
18
BC9
SOFTWARE
THR C:198 , THR C:199 , THR C:200 , ASN C:232 , GLY C:261 , GLY C:263 , ASP C:264 , VAL C:265 , SER C:283 , GLU C:284 , VAL C:285 , ASP C:286 , CYS C:289 , THR C:317 , GLY C:318 , ASN C:319 , ILE C:322 , ILE C:340 , GLY C:341 , HIS C:342 , LEU C:383 , ASN C:385 , HIS C:392 , ADN C:501 , HOH C:606 , HOH C:613 , HOH C:622 , HOH C:743 , HOH C:750 , HOH C:766 , LYS D:467 , TYR D:471
BINDING SITE FOR RESIDUE NAD C 503
19
CC1
SOFTWARE
LEU C:427 , LYS C:429 , ASP C:432 , ASP C:469 , ARG D:472
BINDING SITE FOR RESIDUE GOL C 504
20
CC2
SOFTWARE
HOH A:1026 , LYS C:106 , ARG C:246 , GLY C:387 , ASN C:388 , ALA C:389 , HOH C:739 , HOH C:845
BINDING SITE FOR RESIDUE GOL C 505
21
CC3
SOFTWARE
ARG B:274 , GLY B:297 , ARG C:274 , GLY C:277 , CYS C:278 , ARG C:279 , HOH C:619 , HOH C:725 , HOH C:765 , HOH C:820
BINDING SITE FOR RESIDUE GOL C 506
22
CC4
SOFTWARE
GLY C:459 , PRO C:465 , LYS C:467 , HOH C:679 , HOH C:883
BINDING SITE FOR RESIDUE GOL C 507
23
CC5
SOFTWARE
ASP C:344 , ARG C:353 , HOH C:690
BINDING SITE FOR RESIDUE ACT C 508
24
CC6
SOFTWARE
LYS C:467 , TYR C:471 , ASP D:231 , ASN D:232 , GLY D:263 , ASP D:264 , VAL D:265 , SER D:283 , GLU D:284 , VAL D:285 , ASP D:286 , CYS D:289 , THR D:317 , GLY D:318 , ASN D:319 , ILE D:322 , ILE D:340 , GLY D:341 , HIS D:342 , ASN D:385 , HIS D:392 , HOH D:713 , HOH D:717 , HOH D:718 , HOH D:720 , HOH D:728 , HOH D:780 , HOH D:813 , HOH D:825
BINDING SITE FOR RESIDUE NAD D 501
25
CC7
SOFTWARE
HOH C:926 , LEU D:427 , LYS D:429 , ASP D:432 , ASP D:469 , HOH D:743 , HOH D:811
BINDING SITE FOR RESIDUE GOL D 502
26
CC8
SOFTWARE
ASN D:83 , ILE D:84 , TYR D:113 , ASP D:138 , GLU D:164
BINDING SITE FOR RESIDUE GOL D 503
27
CC9
SOFTWARE
LEU D:233 , ARG D:237 , ALA D:271 , HOH D:732 , HOH D:735 , HOH D:818 , HOH D:847
BINDING SITE FOR RESIDUE GOL D 504
28
DC1
SOFTWARE
GLU C:449 , LEU C:450 , GLN C:462 , HOH C:658 , LYS D:452 , ASP D:456 , HOH D:973
BINDING SITE FOR RESIDUE GOL D 505
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info 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
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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
(0, 0)
Info
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Sorry, no Info available
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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
all PFAM domains
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Sorry, no Info available
[
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