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3WCW
Asym. Unit
Info
Asym.Unit (209 KB)
Biol.Unit 1 (590 KB)
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(1)
Title
:
THE STRUCTURE OF A DEOXYGENATED 400 KDA HEMOGLOBIN PROVIDES A MORE ACCURATE DESCRIPTION OF THE COOPERATIVE MECHANISM OF GIANT HEMOGLOBINS: MG BOUND FORM
Authors
:
N. Numoto, T. Nakagawa, R. Ohara, T. Hasegawa, A. Kita, T. Yoshida, T. Ma K. Imai, Y. Fukumori, K. Miki
Date
:
01 Jun 13 (Deposition) - 04 Jun 14 (Release) - 06 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (3x)
Keywords
:
Globin Fold, Oxygen Transport, Oxygen Binding, Blood
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Numoto, T. Nakagawa, R. Ohara, T. Hasegawa, A. Kita, T. Yoshida, T. Maruyama, K. Imai, Y. Fukumori, K. Miki
The Structure Of A Deoxygenated 400 Kda Haemoglobin Reveals Ternary- And Quaternary-Structural Changes Of Giant Haemoglobins
Acta Crystallogr. , Sect. D V. 70 1823 2014
[
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Hetero Components
(6, 31)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
1b: ALPHA-L-FUCOSE (FUCb)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
2f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
2h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
3a: ALPHA-D-MANNOSE (MANa)
3b: ALPHA-D-MANNOSE (MANb)
3c: ALPHA-D-MANNOSE (MANc)
3d: ALPHA-D-MANNOSE (MANd)
3e: ALPHA-D-MANNOSE (MANe)
3f: ALPHA-D-MANNOSE (MANf)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6a: OXYGEN MOLECULE (OXYa)
6b: OXYGEN MOLECULE (OXYb)
6c: OXYGEN MOLECULE (OXYc)
6d: OXYGEN MOLECULE (OXYd)
6e: OXYGEN MOLECULE (OXYe)
6f: OXYGEN MOLECULE (OXYf)
6g: OXYGEN MOLECULE (OXYg)
6h: OXYGEN MOLECULE (OXYh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
2
HEM
8
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
MAN
6
Ligand/Ion
ALPHA-D-MANNOSE
4
MG
3
Ligand/Ion
MAGNESIUM ION
5
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
OXY
8
Ligand/Ion
OXYGEN MOLECULE
[
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Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:45 , PHE A:46 , SER A:48 , VAL A:49 , ARG A:65 , GLN A:93 , HIS A:94 , ARG A:97 , LEU A:99 , ASN A:103 , PHE A:104 , PHE A:107 , ILE A:135 , ILE A:139 , ASP A:143 , OXY A:202 , HOH A:310 , HIS D:94 , GLN D:98
BINDING SITE FOR RESIDUE HEM A 201
02
AC2
SOFTWARE
TRP A:32 , PHE A:46 , HIS A:62 , VAL A:66 , HEM A:201
BINDING SITE FOR RESIDUE OXY A 202
03
AC3
SOFTWARE
HOH A:328 , HOH A:341
BINDING SITE FOR RESIDUE MG A 203
04
AC4
SOFTWARE
MET B:46 , PHE B:47 , ARG B:49 , ARG B:66 , GLN B:94 , HIS B:95 , ARG B:98 , VAL B:100 , TYR B:105 , VAL B:108 , OXY B:202 , HOH B:321 , HIS C:94 , GLN C:98
BINDING SITE FOR RESIDUE HEM B 201
05
AC5
SOFTWARE
TRP B:33 , PHE B:47 , HIS B:63 , VAL B:67 , HEM B:201
BINDING SITE FOR RESIDUE OXY B 202
06
AC6
SOFTWARE
ASN B:106 , GLU B:109 , ASP B:135
BINDING SITE FOR RESIDUE MG B 203
07
AC7
SOFTWARE
HIS B:90 , GLN B:94 , LEU C:50 , PHE C:51 , ARG C:53 , VAL C:54 , ARG C:70 , VAL C:71 , LEU C:75 , GLN C:98 , HIS C:99 , ARG C:102 , GLY C:109 , PHE C:110 , MET C:144 , OXY C:201 , HOH C:302
BINDING SITE FOR RESIDUE HEM C 200
08
AC8
SOFTWARE
PHE C:37 , PHE C:51 , HIS C:67 , VAL C:71 , HEM C:200
BINDING SITE FOR RESIDUE OXY C 201
09
AC9
SOFTWARE
HIS A:89 , GLN A:93 , SER D:47 , LEU D:50 , PHE D:51 , ASN D:53 , VAL D:54 , HIS D:67 , ARG D:70 , VAL D:71 , GLN D:98 , HIS D:99 , ARG D:102 , LEU D:105 , TYR D:109 , PHE D:110 , OXY D:202 , HOH D:306 , HOH D:321
BINDING SITE FOR RESIDUE HEM D 201
10
BC1
SOFTWARE
PHE D:37 , PHE D:51 , HIS D:67 , VAL D:71 , HEM D:201
BINDING SITE FOR RESIDUE OXY D 202
11
BC2
SOFTWARE
LEU E:45 , PHE E:46 , SER E:48 , VAL E:49 , ARG E:65 , GLN E:93 , HIS E:94 , ARG E:97 , LEU E:99 , ASN E:103 , PHE E:104 , PHE E:107 , ILE E:139 , OXY E:201 , HOH E:330 , HIS H:94 , GLN H:98
BINDING SITE FOR RESIDUE HEM E 200
12
BC3
SOFTWARE
TRP E:32 , PHE E:46 , HIS E:62 , VAL E:66 , HEM E:200
BINDING SITE FOR RESIDUE OXY E 201
13
BC4
SOFTWARE
MET F:46 , PHE F:47 , ARG F:49 , HIS F:63 , ARG F:66 , VAL F:67 , GLN F:94 , HIS F:95 , ARG F:98 , VAL F:100 , TYR F:105 , VAL F:108 , OXY F:202 , HIS G:94 , GLN G:98
BINDING SITE FOR RESIDUE HEM F 201
14
BC5
SOFTWARE
TRP F:33 , PHE F:47 , HIS F:63 , VAL F:67 , HEM F:201
BINDING SITE FOR RESIDUE OXY F 202
15
BC6
SOFTWARE
ASN F:106 , GLU F:109 , ASP F:135
BINDING SITE FOR RESIDUE MG F 203
16
BC7
SOFTWARE
HIS F:90 , GLN F:94 , LEU G:50 , PHE G:51 , ARG G:53 , HIS G:67 , ARG G:70 , VAL G:71 , LEU G:75 , GLN G:98 , HIS G:99 , ARG G:102 , VAL G:105 , GLY G:109 , PHE G:110 , ILE G:113 , MET G:144 , OXY G:201
BINDING SITE FOR RESIDUE HEM G 200
17
BC8
SOFTWARE
PHE G:51 , HIS G:67 , VAL G:71 , HEM G:200
BINDING SITE FOR RESIDUE OXY G 201
18
BC9
SOFTWARE
HIS E:89 , GLN E:93 , LEU H:50 , PHE H:51 , ASN H:53 , VAL H:54 , HIS H:67 , ARG H:70 , GLN H:98 , HIS H:99 , ARG H:102 , TYR H:109 , PHE H:110 , OXY H:202
BINDING SITE FOR RESIDUE HEM H 201
19
CC1
SOFTWARE
PHE H:37 , PHE H:51 , HIS H:67 , VAL H:71 , HEM H:201
BINDING SITE FOR RESIDUE OXY H 202
20
CC2
SOFTWARE
ASP A:81 , GLU D:48 , ASN D:58 , SER D:61 , HOH D:320
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 58 RESIDUES 203 TO 208
21
CC3
SOFTWARE
ASP E:81 , ASN H:58 , SER H:61
BINDING SITE FOR CHAIN H OF SUGAR BOUND TO ASN H 58 RESIDUES 203 TO 208
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
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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)
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Sorry, no Info available
[
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CATH Domains
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Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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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
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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
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