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2PMV
Asym. Unit
Info
Asym.Unit (222 KB)
Biol.Unit 1 (66 KB)
Biol.Unit 2 (46 KB)
Biol.Unit 3 (66 KB)
Biol.Unit 4 (46 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN INTRINSIC FACTOR- COBALAMIN COMPLEX AT 2.6 A RESOLUTION
Authors
:
F. S. Mathews, M. M. Gordon, Z. Chen, K. R. Rajashankar, S. E. Ealick, D. H N. Sukumar
Date
:
23 Apr 07 (Deposition) - 30 Oct 07 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Cobalamin Transport Protein Alpha6-Alpha6 Motif Two Domain Protein, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. S. Mathews, M. M. Gordon, Z. Chen, K. R. Rajashankar, S. E. Ealick, D. H. Alpers, N. Sukumar
Crystal Structure Of Human Intrinsic Factor: Cobalamin Complex At 2. 6-A Resolution
Proc. Natl. Acad. Sci. Usa V. 104 17311 2007
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B12
2
Ligand/Ion
COBALAMIN
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:303 , ASN A:395 , THR A:397 , NAG A:902
BINDING SITE FOR RESIDUE NAG A 901
2
AC2
SOFTWARE
NAG A:901
BINDING SITE FOR RESIDUE NAG A 902
3
AC3
SOFTWARE
GLN C:303 , ASN C:395 , THR C:397 , NAG C:902 , HOH C:1216
BINDING SITE FOR RESIDUE NAG C 901
4
AC4
SOFTWARE
NAG C:901
BINDING SITE FOR RESIDUE NAG C 902
5
AC5
SOFTWARE
THR A:70 , GLY A:72 , HIS A:73 , TYR A:115 , ASP A:153 , ASP A:204 , TYR A:206 , SER A:207 , GLN A:252 , THR A:346 , SER A:347 , TRP A:348 , GLY A:349 , LEU A:350 , VAL A:351 , VAL A:352 , TYR A:367 , TRP A:368 , GLN A:369 , PHE A:370 , LEU A:377 , ASN A:378 , GLU A:379 , GLY A:380 , TYR A:399 , HOH A:1020 , HOH A:1032 , HOH A:1033 , HOH A:1035 , HOH A:1079
BINDING SITE FOR RESIDUE B12 A 1001
6
AC6
SOFTWARE
THR C:70 , GLY C:72 , HIS C:73 , TYR C:115 , ASP C:153 , ASP C:204 , TYR C:206 , SER C:207 , LEU C:210 , GLN C:252 , THR C:346 , SER C:347 , TRP C:348 , GLY C:349 , LEU C:350 , VAL C:351 , VAL C:352 , VAL C:362 , TYR C:367 , TRP C:368 , GLN C:369 , PHE C:370 , PRO C:376 , LEU C:377 , ASN C:378 , GLU C:379 , GLY C:380 , TYR C:399 , HOH C:1099 , HOH C:1109 , HOH C:1113 , HOH C:1115 , HOH C:1122 , HOH C:1166 , HOH C:1175
BINDING SITE FOR RESIDUE B12 C 1002
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SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_022743 (S28L, chain A/B/C/D, )
2: VAR_048753 (G47R, chain A/B/C/D, )
3: VAR_022744 (N237S, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_022743
S
46
L
IF_HUMAN
Disease (IFD)
---
A/B/C/D
S
28
L
2
UniProt
VAR_048753
G
65
R
IF_HUMAN
Polymorphism
11825834
A/B/C/D
G
47
R
3
UniProt
VAR_022744
N
255
S
IF_HUMAN
Polymorphism
35867471
A/B/C/D
N
237
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: COBALAMIN_BINDING (A:151-164,B:151-164,C:151-164,D:15...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COBALAMIN_BINDING
PS00468
Eukaryotic cobalamin-binding proteins signature.
IF_HUMAN
169-182
4
A:151-164
B:151-164
C:151-164
D:151-164
[
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Exons
(9, 32)
Info
All Exons
Exon 1.1a (A:7-9 | B:7-9 | C:7-9 | D:7-9)
Exon 1.2 (A:9-68 | B:9-68 | C:9-68 | D:9-68)
Exon 1.3a (A:68-106 | B:68-106 | C:68-106 | D...)
Exon 1.3c (A:106-153 | B:106-153 | C:106-153 ...)
Exon 1.4a (A:153-213 | B:153-213 | C:153-213 ...)
Exon 1.5 (A:214-273 | B:214-273 | C:214-273 ...)
Exon 1.6a (A:273-340 (gaps) | B:273-273 | C:2...)
Exon 1.7a (A:340-380 | - | C:340-380 | -)
Exon 1.8b (A:380-399 | - | C:380-399 | -)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3a
04: Boundary 1.3a/1.3c
05: Boundary 1.3c/1.4a
06: Boundary 1.4a/1.5
07: Boundary 1.5/1.6a
08: Boundary 1.6a/1.7a
09: Boundary 1.7a/1.8b
10: Boundary 1.8b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000257248
1a
ENSE00001170003
chr11:
59612974-59612848
127
IF_HUMAN
1-27
27
4
A:7-9
B:7-9
C:7-9
D:7-9
3
3
3
3
1.2
ENST00000257248
2
ENSE00000916274
chr11:
59611528-59611352
177
IF_HUMAN
27-86
60
4
A:9-68
B:9-68
C:9-68
D:9-68
60
60
60
60
1.3a
ENST00000257248
3a
ENSE00000916273
chr11:
59610614-59610501
114
IF_HUMAN
86-124
39
4
A:68-106
B:68-106
C:68-106
D:68-106
39
39
39
39
1.3c
ENST00000257248
3c
ENSE00000916272
chr11:
59610056-59609916
141
IF_HUMAN
124-171
48
4
A:106-153
B:106-153
C:106-153
D:106-153
48
48
48
48
1.4a
ENST00000257248
4a
ENSE00000916271
chr11:
59608797-59608616
182
IF_HUMAN
171-231
61
4
A:153-213
B:153-213
C:153-213
D:153-213
61
61
61
61
1.5
ENST00000257248
5
ENSE00000916270
chr11:
59604824-59604647
178
IF_HUMAN
232-291
60
4
A:214-273
B:214-273
C:214-273
D:214-273
60
60
60
60
1.6a
ENST00000257248
6a
ENSE00000916269
chr11:
59603482-59603281
202
IF_HUMAN
291-358
68
4
A:273-340 (gaps)
B:273-273
C:273-340 (gaps)
D:273-273
68
1
68
1
1.7a
ENST00000257248
7a
ENSE00000916268
chr11:
59599269-59599151
119
IF_HUMAN
358-398
41
2
A:340-380
-
C:340-380
-
41
-
41
-
1.8b
ENST00000257248
8b
ENSE00002164105
chr11:
59597018-59596741
278
IF_HUMAN
398-417
20
2
A:380-399
-
C:380-399
-
20
-
20
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cobalamin_bind_2pmvD01 (D:7-273)
1b: PFAM_Cobalamin_bind_2pmvD02 (D:7-273)
1c: PFAM_Cobalamin_bind_2pmvD03 (D:7-273)
1d: PFAM_Cobalamin_bind_2pmvD04 (D:7-273)
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Clans
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Organisms
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)
(
)
Clan
:
6_Hairpin
(120)
Family
:
Cobalamin_bind
(3)
Homo sapiens (Human)
(2)
1a
Cobalamin_bind-2pmvD01
D:7-273
1b
Cobalamin_bind-2pmvD02
D:7-273
1c
Cobalamin_bind-2pmvD03
D:7-273
1d
Cobalamin_bind-2pmvD04
D:7-273
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