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2GTL
Asym. Unit
Info
Asym.Unit (383 KB)
Biol.Unit 1, α-C (4.2 MB)
Biol.Unit 1 (4.2 MB)
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(1)
Title
:
LUMBRICUS ERYTHROCRUORIN AT 3.5A RESOLUTION
Authors
:
W. E. Royer Jr. , H. Sharma, K. Strand, J. E. Knapp, B. Bhyravbhatla
Date
:
28 Apr 06 (Deposition) - 18 Jul 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O (12x)
Keywords
:
Annelid Erythrocruorins, Respiratory Protein, Hexagonal Bilayer, Dihedral D6 Symmetry, Triple Stranded Helical Coils, Oxygen Storage/Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. E. Royer Jr. , H. Sharma, K. Strand, J. E. Knapp, B. Bhyravbhatla
Lumbricus Erythrocruorin At 3. 5 A Resolution: Architecture Of A Megadalton Respiratory Complex.
Structure V. 14 1167 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 29)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: CARBON MONOXIDE (CMOa)
2b: CARBON MONOXIDE (CMOb)
2c: CARBON MONOXIDE (CMOc)
2d: CARBON MONOXIDE (CMOd)
2e: CARBON MONOXIDE (CMOe)
2f: CARBON MONOXIDE (CMOf)
2g: CARBON MONOXIDE (CMOg)
2h: CARBON MONOXIDE (CMOh)
2i: CARBON MONOXIDE (CMOi)
2j: CARBON MONOXIDE (CMOj)
2k: CARBON MONOXIDE (CMOk)
2l: CARBON MONOXIDE (CMOl)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
3f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
3g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
3h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
3i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
3j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
3k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
3l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CMO
12
Ligand/Ion
CARBON MONOXIDE
3
HEM
12
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU M:81 , ASP M:84 , GLU M:86 , ASP M:88 , ASP M:94 , GLU M:95
BINDING SITE FOR RESIDUE CA M 250
02
AC2
SOFTWARE
GLU G:9 , ASP G:86 , ASP M:122
BINDING SITE FOR RESIDUE CA M 251
03
AC3
SOFTWARE
ARG N:123 , SER N:153 , SER N:164 , HIS N:190 , ARG N:209
BINDING SITE FOR RESIDUE ZN M 252
04
AC4
SOFTWARE
LEU N:81 , ASP N:84 , HIS N:86 , ASP N:88 , ASP N:94 , GLU N:95
BINDING SITE FOR RESIDUE CA N 250
05
AC5
SOFTWARE
PHE O:81 , ASP O:84 , HIS O:86 , ASP O:88 , ASP O:94 , GLU O:95
BINDING SITE FOR RESIDUE CA O 250
06
AC6
SOFTWARE
PHE A:39 , PHE A:53 , HIS A:69 , VAL A:73 , HEM A:160
BINDING SITE FOR RESIDUE CMO A 161
07
AC7
SOFTWARE
TRP B:34 , PHE B:48 , HIS B:64 , VAL B:68 , HEM B:160
BINDING SITE FOR RESIDUE CMO B 161
08
AC8
SOFTWARE
PHE C:54 , HIS C:70 , ILE C:74 , HEM C:160
BINDING SITE FOR RESIDUE CMO C 161
09
AC9
SOFTWARE
TRP D:39 , PHE D:53 , HIS D:69 , VAL D:73 , HEM D:160
BINDING SITE FOR RESIDUE CMO D 161
10
BC1
SOFTWARE
PHE E:39 , PHE E:53 , HIS E:69 , VAL E:73 , HEM E:160
BINDING SITE FOR RESIDUE CMO E 161
11
BC2
SOFTWARE
TRP F:34 , PHE F:48 , HIS F:64 , VAL F:68 , HEM F:160
BINDING SITE FOR RESIDUE CMO F 161
12
BC3
SOFTWARE
PHE G:54 , HIS G:70 , ILE G:74 , HEM G:160
BINDING SITE FOR RESIDUE CMO G 161
13
BC4
SOFTWARE
TRP H:39 , PHE H:53 , HIS H:69 , VAL H:73 , HEM H:160
BINDING SITE FOR RESIDUE CMO H 161
14
BC5
SOFTWARE
PHE I:39 , PHE I:53 , HIS I:69 , VAL I:73 , HEM I:160
BINDING SITE FOR RESIDUE CMO I 161
15
BC6
SOFTWARE
TRP J:34 , PHE J:48 , HIS J:64 , VAL J:68 , HEM J:160
BINDING SITE FOR RESIDUE CMO J 161
16
BC7
SOFTWARE
PHE K:54 , HIS K:70 , ILE K:74 , HEM K:160
BINDING SITE FOR RESIDUE CMO K 161
17
BC8
SOFTWARE
TRP L:39 , PHE L:53 , HIS L:69 , VAL L:73 , HEM L:160
BINDING SITE FOR RESIDUE CMO L 161
18
BC9
SOFTWARE
PHE A:53 , ARG A:55 , VAL A:56 , HIS A:69 , ARG A:72 , HIS A:101 , ARG A:104 , TYR A:111 , PHE A:112 , PHE A:139 , CMO A:161 , HIS D:96
BINDING SITE FOR RESIDUE HEM A 160
19
CC1
SOFTWARE
LEU B:47 , PHE B:48 , ARG B:50 , VAL B:68 , GLN B:95 , HIS B:96 , ARG B:99 , ILE B:101 , TYR B:105 , PHE B:106 , PHE B:109 , ILE B:141 , CMO B:161 , HIS C:97 , GLN C:101
BINDING SITE FOR RESIDUE HEM B 160
20
CC2
SOFTWARE
HIS B:91 , PHE C:54 , ARG C:56 , VAL C:57 , HIS C:70 , ARG C:73 , LEU C:78 , GLN C:101 , HIS C:102 , ARG C:105 , HIS C:112 , PHE C:113 , PHE C:116 , LEU C:144 , CMO C:161
BINDING SITE FOR RESIDUE HEM C 160
21
CC3
SOFTWARE
HIS A:96 , GLN A:100 , PRO D:52 , PHE D:53 , ARG D:55 , GLN D:100 , HIS D:101 , ARG D:104 , PHE D:110 , PHE D:111 , PHE D:114 , CMO D:161
BINDING SITE FOR RESIDUE HEM D 160
22
CC4
SOFTWARE
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:161 , HIS H:96
BINDING SITE FOR RESIDUE HEM E 160
23
CC5
SOFTWARE
LEU F:47 , PHE F:48 , ARG F:50 , VAL F:68 , GLN F:95 , HIS F:96 , ARG F:99 , ILE F:101 , TYR F:105 , PHE F:106 , PHE F:109 , ILE F:141 , CMO F:161 , HIS G:97 , GLN G:101
BINDING SITE FOR RESIDUE HEM F 160
24
CC6
SOFTWARE
HIS F:91 , PHE G:54 , ARG G:56 , VAL G:57 , HIS G:70 , ARG G:73 , LEU G:78 , 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:161
BINDING SITE FOR RESIDUE HEM G 160
25
CC7
SOFTWARE
HIS E:96 , GLN E:100 , PHE H:53 , ARG H:55 , GLN H:100 , HIS H:101 , ARG H:104 , PHE H:110 , PHE H:111 , PHE H:114 , CMO H:161
BINDING SITE FOR RESIDUE HEM H 160
26
CC8
SOFTWARE
PHE I:53 , ARG I:55 , VAL I:56 , HIS I:69 , HIS I:101 , ARG I:104 , TYR I:111 , PHE I:112 , PHE I:139 , CMO I:161 , HIS L:96
BINDING SITE FOR RESIDUE HEM I 160
27
CC9
SOFTWARE
LEU J:47 , PHE J:48 , ARG J:50 , VAL J:68 , GLN J:95 , HIS J:96 , ARG J:99 , ILE J:101 , TYR J:105 , PHE J:106 , PHE J:109 , ILE J:141 , CMO J:161 , HIS K:97 , GLN K:101
BINDING SITE FOR RESIDUE HEM J 160
28
DC1
SOFTWARE
HIS J:91 , PHE K:54 , ARG K:56 , VAL K:57 , HIS K:70 , ARG K:73 , LEU K:78 , GLN K:101 , HIS K:102 , ARG K:105 , HIS K:112 , PHE K:113 , PHE K:116 , LEU K:144 , CMO K:161
BINDING SITE FOR RESIDUE HEM K 160
29
DC2
SOFTWARE
HIS I:96 , GLN I:100 , PRO L:52 , PHE L:53 , ARG L:55 , GLN L:100 , HIS L:101 , ARG L:104 , PHE L:110 , PHE L:111 , PHE L:114 , CMO L:161
BINDING SITE FOR RESIDUE HEM L 160
[
close Site info
]
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
View:
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Label:
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
(13, 21)
Info
All SCOP Domains
01a: SCOP_d2gtld1 (D:8-147)
01b: SCOP_d2gtlh1 (H:8-147)
01c: SCOP_d2gtll1 (L:8-147)
02a: SCOP_d2gtlb1 (B:1-145)
02b: SCOP_d2gtlf1 (F:1-145)
02c: SCOP_d2gtlj1 (J:1-145)
03a: SCOP_d2gtlc1 (C:3-151)
03b: SCOP_d2gtlg1 (G:3-151)
03c: SCOP_d2gtlk1 (K:3-151)
04a: SCOP_d2gtla1 (A:5-151)
04b: SCOP_d2gtle1 (E:5-151)
04c: SCOP_d2gtli1 (I:5-151)
05a: SCOP_d2gtln1 (N:102-229)
06a: SCOP_d2gtlo1 (O:101-222)
07a: SCOP_d2gtlm1 (M:102-225)
08a: SCOP_d2gtln3 (N:10-60)
09a: SCOP_d2gtlo3 (O:8-59)
10a: SCOP_d2gtlm3 (M:9-59)
11a: SCOP_d2gtln2 (N:61-101)
12a: SCOP_d2gtlo2 (O:60-100)
13a: SCOP_d2gtlm2 (M:60-101)
View:
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Classes
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)
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(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
01a
d2gtld1
D:8-147
01b
d2gtlh1
H:8-147
01c
d2gtll1
L:8-147
Protein domain
:
Extracellular dodecameric hemoglobin (erythrocruorin), subunit II (globin B)
(2)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(2)
02a
d2gtlb1
B:1-145
02b
d2gtlf1
F:1-145
02c
d2gtlj1
J:1-145
Protein domain
:
Extracellular dodecameric hemoglobin (erythrocruorin), subunit III (globin C)
(2)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(2)
03a
d2gtlc1
C:3-151
03b
d2gtlg1
G:3-151
03c
d2gtlk1
K:3-151
Protein domain
:
Extracellular dodecameric hemoglobin (erythrocruorin), subunit IV (globin A)
(2)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(2)
04a
d2gtla1
A:5-151
04b
d2gtle1
E:5-151
04c
d2gtli1
I:5-151
Class
:
All beta proteins
(24004)
Fold
:
Streptavidin-like
(225)
Superfamily
:
Extracellular hemoglobin linker subunit, receptor domain
(3)
Family
:
Extracellular hemoglobin linker subunit, receptor domain
(3)
Protein domain
:
Extracellular hemoglobin linker l2 subunit
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
05a
d2gtln1
N:102-229
Protein domain
:
Extracellular hemoglobin linker l3 subunit
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
06a
d2gtlo1
O:101-222
Protein domain
:
Hemoglobin linker chain l1
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
07a
d2gtlm1
M:102-225
Class
:
Coiled coil proteins
(689)
Fold
:
Parallel coiled-coil
(407)
Superfamily
:
Heterotrimerisation domain of extracellular hemoglobin linker subunits
(3)
Family
:
Heterotrimerisation domain of extracellular hemoglobin linker subunits
(3)
Protein domain
:
Extracellular hemoglobin linker l2 subunit
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
08a
d2gtln3
N:10-60
Protein domain
:
Extracellular hemoglobin linker l3
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
09a
d2gtlo3
O:8-59
Protein domain
:
Hemoglobin linker chain l1
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
10a
d2gtlm3
M:9-59
Class
:
Small proteins
(3458)
Fold
:
LDL receptor-like module
(20)
Superfamily
:
LDL receptor-like module
(20)
Family
:
LDL receptor-like module
(19)
Protein domain
:
Extracellular hemoglobin linker l2 subunit
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
11a
d2gtln2
N:61-101
Protein domain
:
Extracellular hemoglobin linker l3 subunit
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
12a
d2gtlo2
O:60-100
Protein domain
:
Hemoglobin linker chain l1
(1)
Common earthworm (Lumbricus terrestris) [TaxId: 6398]
(1)
13a
d2gtlm2
M:60-101
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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all PFAM domains
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