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1X9F
Asym. Unit
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Asym.Unit (311 KB)
Biol.Unit 1 (301 KB)
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(1)
Title
:
HEMOGLOBIN DODECAMER FROM LUMBRICUS ERYTHROCRUORIN
Authors
:
K. Strand, J. E. Knapp, B. Bhyravbhatla, W. E. Royer Jr.
Date
:
20 Aug 04 (Deposition) - 30 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Crystal; Dodecamer; Allosteric, Oxygen Storage/Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Strand, J. E. Knapp, B. Bhyravbhatla, W. E. Royer Jr.
Crystal Structure Of The Hemoglobin Dodecamer From Lumbricus Erythrocruorin: Allosteric Core Of Giant Annelid Respiratory Complexes
J. Mol. Biol. V. 344 119 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 27)
Info
All Hetero Components
1a: CARBON MONOXIDE (CMOa)
1b: CARBON MONOXIDE (CMOb)
1c: CARBON MONOXIDE (CMOc)
1d: CARBON MONOXIDE (CMOd)
1e: CARBON MONOXIDE (CMOe)
1f: CARBON MONOXIDE (CMOf)
1g: CARBON MONOXIDE (CMOg)
1h: CARBON MONOXIDE (CMOh)
1i: CARBON MONOXIDE (CMOi)
1j: CARBON MONOXIDE (CMOj)
1k: CARBON MONOXIDE (CMOk)
1l: CARBON MONOXIDE (CMOl)
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)
2i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
2j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
2k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
2l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CMO
12
Ligand/Ion
CARBON MONOXIDE
2
HEM
12
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
PO4
3
Ligand/Ion
PHOSPHATE ION
[
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]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG F:50 , ASP G:96 , HIS G:97 , HIS G:100
BINDING SITE FOR RESIDUE PO4 G 154
02
AC2
SOFTWARE
ARG J:50 , ASP K:96 , HIS K:97 , HIS K:100
BINDING SITE FOR RESIDUE PO4 K 154
03
AC3
SOFTWARE
ARG B:50 , HIS C:97 , HIS C:100
BINDING SITE FOR RESIDUE PO4 C 154
04
AC4
SOFTWARE
LEU A:52 , PHE A:53 , ARG A:55 , VAL A:56 , ARG A:72 , HIS A:101 , ARG A:104 , TYR A:111 , PHE A:112 , PHE A:139 , CMO A:1161 , HOH A:1162 , HIS D:89 , GLN D:93
BINDING SITE FOR RESIDUE HEM A 160
05
AC5
SOFTWARE
PHE A:39 , PHE A:53 , HIS A:69 , VAL A:73 , HEM A:160
BINDING SITE FOR RESIDUE CMO A 1161
06
AC6
SOFTWARE
LEU B:47 , PHE B:48 , ARG B:50 , ARG B:67 , LEU B:92 , GLN B:95 , HIS B:96 , ARG B:99 , ILE B:101 , PHE B:109 , GLU B:138 , CMO B:1162 , HOH B:1191 , HIS C:97 , GLN C:101
BINDING SITE FOR RESIDUE HEM B 160
07
AC7
SOFTWARE
TRP B:34 , PHE B:48 , HIS B:64 , VAL B:68 , HEM B:160
BINDING SITE FOR RESIDUE CMO B 1162
08
AC8
SOFTWARE
HIS B:91 , GLN B:95 , LEU C:53 , PHE C:54 , ARG C:56 , VAL C:57 , ARG C:73 , ILE C:74 , GLY C:77 , LEU C:78 , LEU C:98 , GLN C:101 , HIS C:102 , ARG C:105 , VAL C:108 , HIS C:112 , PHE C:113 , PHE C:116 , LEU C:144 , CMO C:1163 , HOH C:1171 , HOH C:1178
BINDING SITE FOR RESIDUE HEM C 160
09
AC9
SOFTWARE
LEU C:40 , HIS C:70 , ILE C:74 , HEM C:160
BINDING SITE FOR RESIDUE CMO C 1163
10
BC1
SOFTWARE
HIS A:96 , GLN A:100 , PRO D:45 , PHE D:46 , ARG D:48 , VAL D:49 , HIS D:62 , ARG D:65 , LEU D:90 , GLN D:93 , HIS D:94 , ARG D:97 , LEU D:99 , PHE D:103 , PHE D:104 , PHE D:107 , ILE D:136 , CMO D:1164 , HOH D:1170 , HOH D:1177
BINDING SITE FOR RESIDUE HEM D 160
11
BC2
SOFTWARE
TRP D:32 , PHE D:46 , HIS D:62 , VAL D:66 , HEM D:160
BINDING SITE FOR RESIDUE CMO D 1164
12
BC3
SOFTWARE
LEU E:52 , PHE E:53 , ARG E:55 , VAL E:56 , ARG E:72 , HIS E:101 , ARG E:104 , TYR E:111 , PHE E:112 , PHE E:139 , CMO E:2161 , HOH E:2166 , HIS H:89 , GLN H:93
BINDING SITE FOR RESIDUE HEM E 160
13
BC4
SOFTWARE
PHE E:39 , PHE E:53 , HIS E:69 , VAL E:73 , HEM E:160
BINDING SITE FOR RESIDUE CMO E 2161
14
BC5
SOFTWARE
LEU F:47 , PHE F:48 , ARG F:50 , ARG F:67 , LEU F:72 , GLN F:95 , HIS F:96 , ARG F:99 , ILE F:101 , PHE F:106 , PHE F:109 , GLU F:138 , ILE F:141 , CMO F:2162 , HOH F:2164 , HIS G:97 , GLN G:101
BINDING SITE FOR RESIDUE HEM F 160
15
BC6
SOFTWARE
TRP F:34 , PHE F:48 , HIS F:64 , VAL F:68 , HEM F:160
BINDING SITE FOR RESIDUE CMO F 2162
16
BC7
SOFTWARE
HIS F:91 , GLN F:95 , LEU G:53 , PHE G:54 , ARG G:56 , VAL G:57 , ARG G:73 , GLY G:77 , LEU G:78 , LEU G:98 , GLN G:101 , HIS G:102 , ARG G:105 , VAL G:108 , HIS G:112 , PHE G:113 , PHE G:116 , LEU G:144 , CMO G:2163 , HOH G:2168
BINDING SITE FOR RESIDUE HEM G 160
17
BC8
SOFTWARE
LEU G:40 , PHE G:54 , HIS G:70 , ILE G:74 , HEM G:160
BINDING SITE FOR RESIDUE CMO G 2163
18
BC9
SOFTWARE
HOH A:1170 , HIS E:96 , GLN E:100 , PRO H:45 , PHE H:46 , ARG H:48 , VAL H:49 , HIS H:62 , ARG H:65 , LEU H:70 , LEU H:90 , GLN H:93 , HIS H:94 , ARG H:97 , LEU H:99 , PHE H:103 , PHE H:104 , PHE H:107 , ILE H:136 , CMO H:2164
BINDING SITE FOR RESIDUE HEM H 160
19
CC1
SOFTWARE
TRP H:32 , PHE H:46 , HIS H:62 , VAL H:66 , HEM H:160
BINDING SITE FOR RESIDUE CMO H 2164
20
CC2
SOFTWARE
LEU I:52 , PHE I:53 , ARG I:55 , VAL I:56 , ARG I:72 , HIS I:101 , ARG I:104 , TYR I:111 , PHE I:112 , PHE I:139 , CMO I:3161 , HOH I:3179 , HOH I:3192 , HIS L:89 , GLN L:93
BINDING SITE FOR RESIDUE HEM I 160
21
CC3
SOFTWARE
PHE I:39 , PHE I:53 , HIS I:69 , VAL I:73 , HEM I:160
BINDING SITE FOR RESIDUE CMO I 3161
22
CC4
SOFTWARE
LEU J:47 , PHE J:48 , ARG J:50 , ARG J:67 , LEU J:72 , GLN J:95 , HIS J:96 , ARG J:99 , ILE J:101 , PHE J:109 , GLU J:138 , ILE J:141 , CMO J:3162 , HIS K:97 , GLN K:101
BINDING SITE FOR RESIDUE HEM J 160
23
CC5
SOFTWARE
TRP J:34 , PHE J:48 , HIS J:64 , VAL J:68 , HEM J:160
BINDING SITE FOR RESIDUE CMO J 3162
24
CC6
SOFTWARE
HIS J:91 , GLN J:95 , LEU K:53 , PHE K:54 , ARG K:56 , VAL K:57 , ARG K:73 , GLY K:77 , LEU K:78 , LEU K:98 , GLN K:101 , HIS K:102 , ARG K:105 , VAL K:108 , HIS K:112 , PHE K:113 , PHE K:116 , LEU K:144 , CMO K:3163
BINDING SITE FOR RESIDUE HEM K 160
25
CC7
SOFTWARE
LEU K:40 , HIS K:70 , ILE K:74 , HEM K:160
BINDING SITE FOR RESIDUE CMO K 3163
26
CC8
SOFTWARE
HIS I:96 , GLN I:100 , PRO L:45 , PHE L:46 , ARG L:48 , VAL L:49 , HIS L:62 , ARG L:65 , LEU L:70 , LEU L:90 , GLN L:93 , HIS L:94 , ARG L:97 , LEU L:99 , PHE L:103 , PHE L:104 , PHE L:107 , ILE L:136 , CMO L:3164 , HOH L:3181
BINDING SITE FOR RESIDUE HEM L 160
27
CC9
SOFTWARE
TRP L:32 , PHE L:46 , HIS L:62 , VAL L:66 , HEM L:160
BINDING SITE FOR RESIDUE CMO L 3164
[
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]
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
(1, 9)
Info
All PROSITE Patterns/Profiles
1: GLOBIN (B:8-137,F:8-137,J:8-137,A:10-139,E...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLOBIN
PS01033
Globin family profile.
GLB2_LUMTE
8-137
3
B:8-137
F:8-137
J:8-137
GLB4_LUMTE
10-139
3
A:10-139
E:10-139
I:10-139
GLB3_LUMTE
56-160
3
C:39-143
G:39-143
K:39-143
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 12)
Info
All SCOP Domains
1a: SCOP_d1x9fd_ (D:)
1b: SCOP_d1x9fh_ (H:)
1c: SCOP_d1x9fl_ (L:)
2a: SCOP_d1x9fb_ (B:)
2b: SCOP_d1x9ff_ (F:)
2c: SCOP_d1x9fj_ (J:)
3a: SCOP_d1x9fc_ (C:)
3b: SCOP_d1x9fg_ (G:)
3c: SCOP_d1x9fk_ (K:)
4a: SCOP_d1x9fa_ (A:)
4b: SCOP_d1x9fe_ (E:)
4c: SCOP_d1x9fi_ (I:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
Globin-like
(1308)
Family
:
Globins
(1157)
Protein domain
:
Extracellular dodecameric hemoglobin (erythrocruorin), subunit D1
(2)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(2)
1a
d1x9fd_
D:
1b
d1x9fh_
H:
1c
d1x9fl_
L:
Protein domain
:
Extracellular dodecameric hemoglobin (erythrocruorin), subunit II (globin B)
(2)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(2)
2a
d1x9fb_
B:
2b
d1x9ff_
F:
2c
d1x9fj_
J:
Protein domain
:
Extracellular dodecameric hemoglobin (erythrocruorin), subunit III (globin C)
(2)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(2)
3a
d1x9fc_
C:
3b
d1x9fg_
G:
3c
d1x9fk_
K:
Protein domain
:
Extracellular dodecameric hemoglobin (erythrocruorin), subunit IV (globin A)
(2)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(2)
4a
d1x9fa_
A:
4b
d1x9fe_
E:
4c
d1x9fi_
I:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_Globin_1x9fJ01 (J:8-114)
1b: PFAM_Globin_1x9fJ02 (J:8-114)
1c: PFAM_Globin_1x9fJ03 (J:8-114)
1d: PFAM_Globin_1x9fK01 (K:11-121)
1e: PFAM_Globin_1x9fK02 (K:11-121)
1f: PFAM_Globin_1x9fK03 (K:11-121)
1g: PFAM_Globin_1x9fI01 (I:11-120)
1h: PFAM_Globin_1x9fI02 (I:11-120)
1i: PFAM_Globin_1x9fI03 (I:11-120)
1j: PFAM_Globin_1x9fL01 (L:6-112)
1k: PFAM_Globin_1x9fL02 (L:6-112)
1l: PFAM_Globin_1x9fL03 (L:6-112)
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Clan
:
Globin
(291)
Family
:
Globin
(264)
Lumbricus terrestris (Common earthworm)
(1)
1a
Globin-1x9fJ01
J:8-114
1b
Globin-1x9fJ02
J:8-114
1c
Globin-1x9fJ03
J:8-114
1d
Globin-1x9fK01
K:11-121
1e
Globin-1x9fK02
K:11-121
1f
Globin-1x9fK03
K:11-121
1g
Globin-1x9fI01
I:11-120
1h
Globin-1x9fI02
I:11-120
1i
Globin-1x9fI03
I:11-120
1j
Globin-1x9fL01
L:6-112
1k
Globin-1x9fL02
L:6-112
1l
Globin-1x9fL03
L:6-112
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