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4KO4
Asym. Unit
Info
Asym.Unit (574 KB)
Biol.Unit 1 (284 KB)
Biol.Unit 2 (287 KB)
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(1)
Title
:
HIGH X-RAY DOSE STRUCTURE OF ANAEROBICALLY PURIFIED DM. BACULATUM [NIFESE]-HYDROGENASE AFTER CRYSTALLIZATION UNDER AIR
Authors
:
A. Volbeda, C. Cavazza, J. C. Fontecilla-Camps
Date
:
11 May 13 (Deposition) - 10 Jul 13 (Release) - 08 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : L,M,S,T
Biol. Unit 1: L,S (1x)
Biol. Unit 2: M,T (1x)
Keywords
:
Nifese-Site, H2 Cleavage/Production, Seleninate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, P. Amara, M. Iannello, A. L. De Lacey, C. Cavazza, J. C. Fontecilla-Camps
Structural Foundations For The O2 Resistance Of Desulfomicrobium Baculatum [Nifese]-Hydrogenase.
Chem. Commun. (Camb. ) V. 49 7061 2013
(for further references see the
PDB file header
)
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Hetero Components
(10, 31)
Info
All Hetero Components
01a: CALCIUM ION (CAa)
01b: CALCIUM ION (CAb)
01c: CALCIUM ION (CAc)
01d: CALCIUM ION (CAd)
01e: CALCIUM ION (CAe)
01f: CALCIUM ION (CAf)
01g: CALCIUM ION (CAg)
01h: CALCIUM ION (CAh)
02a: CHLORIDE ION (CLa)
03a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
03b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
04a: GLYCEROL (GOLa)
04b: GLYCEROL (GOLb)
04c: GLYCEROL (GOLc)
04d: GLYCEROL (GOLd)
05a: HYDROSULFURIC ACID (H2Sa)
05b: HYDROSULFURIC ACID (H2Sb)
06a: NICKEL (II) ION (NIa)
06b: NICKEL (II) ION (NIb)
07a: 2-AMINO-3-SELENINO-PROPIONIC ACID (SE7a)
07b: 2-AMINO-3-SELENINO-PROPIONIC ACID (SE7b)
08a: (SECa)
08b: (SECb)
09a: IRON/SULFUR CLUSTER (SF4a)
09b: IRON/SULFUR CLUSTER (SF4b)
09c: IRON/SULFUR CLUSTER (SF4c)
09d: IRON/SULFUR CLUSTER (SF4d)
09e: IRON/SULFUR CLUSTER (SF4e)
09f: IRON/SULFUR CLUSTER (SF4f)
10a: 3-(OXIDO-LAMBDA~4~-SELANYL)-L-ALAN... (UOXa)
10b: 3-(OXIDO-LAMBDA~4~-SELANYL)-L-ALAN... (UOXb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
CL
1
Ligand/Ion
CHLORIDE ION
3
FCO
2
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
4
GOL
4
Ligand/Ion
GLYCEROL
5
H2S
2
Ligand/Ion
HYDROSULFURIC ACID
6
NI
2
Ligand/Ion
NICKEL (II) ION
7
SE7
2
Mod. Residue
2-AMINO-3-SELENINO-PROPIONIC ACID
8
SEC
2
Mod. Amino Acid
9
SF4
6
Ligand/Ion
IRON/SULFUR CLUSTER
10
UOX
2
Ligand/Ion
3-(OXIDO-LAMBDA~4~-SELANYL)-L-ALANINE
[
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Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS S:208 , CYS S:211 , CYS S:231 , LYS S:232 , CYS S:237 , VAL S:259
BINDING SITE FOR RESIDUE SF4 S 301
02
AC2
SOFTWARE
ARG L:185 , THR S:242 , CYS S:246 , TRP S:251 , CYS S:258 , CYS S:264 , ILE S:265 , CYS S:267
BINDING SITE FOR RESIDUE SF4 S 302
03
AC3
SOFTWARE
ARG L:68 , HIS L:188 , GLY S:17 , CYS S:18 , CYS S:21 , GLY S:124 , THR S:125 , CYS S:126 , GLY S:163 , CYS S:164 , PRO S:165
BINDING SITE FOR RESIDUE SF4 S 303
04
AC4
SOFTWARE
ASP L:87 , GLU S:152 , HOH S:454 , HOH S:455 , HOH S:457 , HOH S:471
BINDING SITE FOR RESIDUE CA S 304
05
AC5
SOFTWARE
ASN S:27 , HIS S:167 , ASN S:252 , ASN S:253 , HOH S:403 , HOH S:431 , HOH S:458
BINDING SITE FOR RESIDUE CL S 305
06
AC6
SOFTWARE
GLU M:31 , ASP M:39 , ARG M:455 , HOH M:1002 , HIS S:30 , ARG S:32 , HOH S:519 , HOH S:566
BINDING SITE FOR RESIDUE GOL S 306
07
AC7
SOFTWARE
ASP L:413 , HOH L:949 , TYR S:62 , ASP S:112 , LYS S:116 , HOH S:547 , HOH S:557 , HOH S:674
BINDING SITE FOR RESIDUE GOL S 307
08
AC8
SOFTWARE
HOH L:900 , HOH L:1093 , HOH S:539 , HOH S:633 , HOH S:651 , HOH S:772
BINDING SITE FOR RESIDUE CA S 308
09
AC9
SOFTWARE
CYS L:73 , HIS L:77 , ALA L:423 , PRO L:424 , ARG L:425 , LEU L:428 , ALA L:447 , THR L:448 , CYS L:495 , NI L:502 , HOH L:606
BINDING SITE FOR RESIDUE FCO L 501
10
BC1
SOFTWARE
CYS L:70 , CYS L:73 , SEC L:492 , GLY L:494 , CYS L:495 , FCO L:501 , HOH L:606 , HOH L:607
BINDING SITE FOR RESIDUE NI L 502
11
BC2
SOFTWARE
GLU L:51 , ILE L:444 , HIS L:498 , HOH L:608 , HOH L:609 , HOH L:610
BINDING SITE FOR RESIDUE CA L 503
12
BC3
SOFTWARE
CYS L:73 , THR L:75 , ALA L:76 , PHE L:105 , ASN L:108 , PRO L:424
BINDING SITE FOR RESIDUE H2S L 504
13
BC4
SOFTWARE
HIS T:208 , CYS T:211 , TYR T:213 , LEU T:214 , CYS T:231 , LYS T:232 , CYS T:237 , GLY T:239 , VAL T:259
BINDING SITE FOR RESIDUE SF4 T 301
14
BC5
SOFTWARE
ARG M:185 , THR T:242 , CYS T:246 , TRP T:251 , CYS T:258 , CYS T:264 , ILE T:265 , CYS T:267
BINDING SITE FOR RESIDUE SF4 T 302
15
BC6
SOFTWARE
ARG M:68 , HIS M:188 , GLY T:17 , CYS T:18 , CYS T:21 , GLY T:124 , THR T:125 , CYS T:126 , GLY T:163 , CYS T:164 , PRO T:165
BINDING SITE FOR RESIDUE SF4 T 303
16
BC7
SOFTWARE
HOH M:614 , HOH M:618 , HOH M:620 , HOH T:506 , HOH T:538 , HOH T:547 , HOH T:579
BINDING SITE FOR RESIDUE CA T 304
17
BC8
SOFTWARE
HOH L:855 , ASP T:271 , GLY T:275 , HOH T:469 , HOH T:499 , HOH T:727 , HOH T:746
BINDING SITE FOR RESIDUE CA T 305
18
BC9
SOFTWARE
ASP T:195 , ASP T:196 , HOH T:475 , HOH T:581 , HOH T:723 , HOH T:731
BINDING SITE FOR RESIDUE CA T 306
19
CC1
SOFTWARE
CYS M:73 , HIS M:77 , ALA M:423 , PRO M:424 , ARG M:425 , LEU M:428 , ALA M:447 , THR M:448 , CYS M:495 , NI M:502 , HOH M:623
BINDING SITE FOR RESIDUE FCO M 501
20
CC2
SOFTWARE
CYS M:70 , CYS M:73 , SEC M:492 , GLY M:494 , CYS M:495 , FCO M:501 , HOH M:623 , HOH M:624
BINDING SITE FOR RESIDUE NI M 502
21
CC3
SOFTWARE
GLU M:51 , ILE M:444 , HIS M:498 , HOH M:625 , HOH M:626 , HOH M:627
BINDING SITE FOR RESIDUE CA M 503
22
CC4
SOFTWARE
CYS M:73 , THR M:75 , ALA M:76 , PHE M:105 , ASN M:108 , PRO M:424
BINDING SITE FOR RESIDUE H2S M 504
23
CC5
SOFTWARE
ALA M:156 , THR M:157 , HOH M:1026
BINDING SITE FOR RESIDUE GOL M 505
24
CC6
SOFTWARE
ASP M:39 , ARG M:455 , GLY M:459 , ARG M:461 , GLU S:35
BINDING SITE FOR RESIDUE GOL M 506
25
CC7
SOFTWARE
ASP M:17 , LEU M:26 , HOH M:768 , ILE T:90 , HOH T:592
BINDING SITE FOR RESIDUE CA M 507
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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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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d4ko4s_ (S:)
1b: SCOP_d4ko4t_ (T:)
2a: SCOP_d4ko4l_ (L:)
2b: SCOP_d4ko4m_ (M:)
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(
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
HydA/Nqo6-like
(51)
Superfamily
:
HydA/Nqo6-like
(51)
Family
:
Nickel-iron hydrogenase, small subunit
(39)
Protein domain
:
automated matches
(23)
Desulfomicrobium baculatum [TaxId: 899]
(6)
1a
d4ko4s_
S:
1b
d4ko4t_
T:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
automated matches
(23)
Desulfomicrobium baculatum [TaxId: 525897]
(6)
2a
d4ko4l_
L:
2b
d4ko4m_
M:
[
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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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Protein & NOT Site
Protein & NOT PROSITE
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