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4UD6
Biol. Unit 3
Info
Asym.Unit (814 KB)
Biol.Unit 1 (274 KB)
Biol.Unit 2 (273 KB)
Biol.Unit 3 (273 KB)
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(1)
Title
:
STRUCTURE OF METHYLVIOLOGEN-TREATED ANAEROBICALLY PURIFIED D. FRUCTOSOVORANS NIFE-HYDROGENASE
Authors
:
A. Volbeda, L. Martin, P. -P. Liebgott, J. C. Fontecilla-Camps
Date
:
08 Dec 14 (Deposition) - 25 Mar 15 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.12
Chains
:
Asym. Unit : A,B,C,Q,R,S
Biol. Unit 1: A,Q (1x)
Biol. Unit 2: C,S (1x)
Biol. Unit 3: B,R (1x)
Keywords
:
Oxidoreductase, Nife-Hydrogenase, Ni-Sib State, Ni-C State
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, L. Martin, P. -P. Liebgott, A. L. De Lacey, J. C. Fontecilla-Camps
[Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation In A Variant With Accrued O2-Tolerance And A Tentative Re-Interpretation Of Ni-Si States.
Metallomics V. 7 710 2015
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Hetero Components
(5, 12)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
1b: S-HYDROXYCYSTEINE (CSOb)
1c: S-HYDROXYCYSTEINE (CSOc)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
2c: FE3-S4 CLUSTER (F3Sc)
3a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
3b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
3c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
4o: GLYCEROL (GOLo)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
6a: NICKEL (II) ION (NIa)
6b: NICKEL (II) ION (NIb)
6c: NICKEL (II) ION (NIc)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
7d: IRON/SULFUR CLUSTER (SF4d)
7e: IRON/SULFUR CLUSTER (SF4e)
7f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
1
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
3
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
4
GOL
7
Ligand/Ion
GLYCEROL
5
MG
-1
Ligand/Ion
MAGNESIUM ION
6
NI
-1
Ligand/Ion
NICKEL (II) ION
7
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
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Sites
(13, 13)
Info
All Sites
01: AC7 (SOFTWARE)
02: AC8 (SOFTWARE)
03: AC9 (SOFTWARE)
04: CC2 (SOFTWARE)
05: CC3 (SOFTWARE)
06: CC4 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC7 (SOFTWARE)
10: CC8 (SOFTWARE)
11: CC9 (SOFTWARE)
12: DC1 (SOFTWARE)
13: DC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC7
SOFTWARE
HIS B:184 , CYS B:187 , ARG B:189 , LEU B:190 , PHE B:193 , CYS B:212 , LEU B:213 , CYS B:218
BINDING SITE FOR RESIDUE SF4 B1265
02
AC8
SOFTWARE
ASN B:225 , CYS B:227 , PHE B:232 , CYS B:245 , LEU B:246 , CYS B:248 , LYS R:225 , GLN R:230
BINDING SITE FOR RESIDUE F3S B1266
03
AC9
SOFTWARE
GLU B:16 , CYS B:17 , CYS B:20 , GLY B:112 , THR B:113 , CYS B:114 , GLY B:146 , CYS B:147 , PRO B:148 , ARG R:70 , HIS R:228
BINDING SITE FOR RESIDUE SF4 B1267
04
CC2
SOFTWARE
GLY R:281 , GLY R:282 , ILE R:283 , GLY R:284 , GLY R:285 , ARG R:319 , HIS R:419 , HOH R:2259
BINDING SITE FOR RESIDUE GOL R1001
05
CC3
SOFTWARE
THR R:286 , SER R:287 , ASN R:288 , ALA R:380 , PRO R:514 , GLU R:517 , HOH R:2225 , HOH R:2380
BINDING SITE FOR RESIDUE GOL R1002
06
CC4
SOFTWARE
ARG R:152 , PRO R:153 , SER R:156 , HOH R:2130 , HOH R:2137 , ALA S:451
BINDING SITE FOR RESIDUE GOL R1003
07
CC5
SOFTWARE
ALA C:103 , GLU R:465 , SER R:466 , LYS R:467 , ARG R:484 , HOH R:2366 , HOH R:2367
BINDING SITE FOR RESIDUE GOL R1004
08
CC6
SOFTWARE
CYS R:75 , VAL R:78 , HIS R:79 , ALA R:474 , PRO R:475 , ARG R:476 , LEU R:479 , VAL R:497 , PRO R:498 , SER R:499 , CSO R:543 , CYS R:546 , NI R:1551
BINDING SITE FOR RESIDUE FCO R1550
09
CC7
SOFTWARE
CYS R:72 , CYS R:75 , CSO R:543 , CYS R:546 , FCO R:1550
BINDING SITE FOR RESIDUE NI R1551
10
CC8
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:2049 , HOH R:2050 , HOH R:2275
BINDING SITE FOR RESIDUE MG R1553
11
CC9
SOFTWARE
ALA B:55 , ASN R:181 , ALA R:182 , TYR R:183 , LEU R:185 , ARG R:529 , HOH R:2389
BINDING SITE FOR RESIDUE GOL R1561
12
DC1
SOFTWARE
LEU B:137 , GLY R:409 , LYS R:410 , HOH R:2336
BINDING SITE FOR RESIDUE GOL R1562
13
DC2
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLN R:310 , GLU R:445 , HOH R:2098 , HOH R:2101 , HOH R:2245
BINDING SITE FOR RESIDUE GOL R1563
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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
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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
(0, 0)
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CATH Domains
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Pfam Domains
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Atom Selection
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Protein & NOT Variant
Protein & NOT Site
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Chain B
Chain R
Asymmetric Unit 1
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Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
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
show bonds with a radius of 100 units (=0.4Å)
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Show PDB file:
Asym.Unit (814 KB)
Header - Asym.Unit
Biol.Unit 1 (274 KB)
Header - Biol.Unit 1
Biol.Unit 2 (273 KB)
Header - Biol.Unit 2
Biol.Unit 3 (273 KB)
Header - Biol.Unit 3
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