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3IKQ
Asym. Unit
Info
Asym.Unit (80 KB)
Biol.Unit 1 (74 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ALPHA 1-2 MANNOBIOSE BOUND TRIMERIC HUMAN LUNG SURFACTANT PROTEIN D
Authors
:
A. K. Shrive, T. J. Greenhough
Date
:
06 Aug 09 (Deposition) - 17 Nov 09 (Release) - 19 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Trimeric Recombinant Fragment, Neck+Crd, Collagen, Disulfide Bond, Extracellular Matrix, Gaseous Exchange, Glycoprotein, Hydroxylation, Lectin, Secreted, Surface Film, Sugar Binding Protein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
A. K. Shrive, C. Martin, I. Burns, J. M. Paterson, J. D. Martin, J. P. Townsend, P. Waters, H. W. Clark, U. Kishore, K. B. M. Reid, T. J. Greenhough
Structural Characterisation Of Ligand-Binding Determinants In Human Lung Surfactant Protein D: Influence Of Asp325
J. Mol. Biol. V. 394 776 2009
(for further references see the
PDB file header
)
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Hetero Components
(2, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
10
Ligand/Ion
CALCIUM ION
2
MAN
3
Ligand/Ion
ALPHA-D-MANNOSE
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:321 , ASN A:323 , GLU A:329 , ASN A:341 , ASP A:342 , MAN A:405
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
ASP A:297 , GLU A:301 , ASP A:324 , GLU A:329 , ASP A:330
BINDING SITE FOR RESIDUE CA A 402
03
AC3
SOFTWARE
HOH A:64 , HOH A:159 , GLU A:301 , ASP A:330
BINDING SITE FOR RESIDUE CA A 403
04
AC4
SOFTWARE
HOH A:156 , GLU A:232 , HOH B:157 , GLU B:232 , HOH C:160 , GLU C:232
BINDING SITE FOR RESIDUE CA A 404
05
AC5
SOFTWARE
GLU A:321 , ASN A:323 , ASP A:325 , GLU A:329 , ASN A:341 , ASP A:342 , ARG A:343 , CA A:401
BINDING SITE FOR RESIDUE MAN A 405
06
AC6
SOFTWARE
GLU B:321 , ASN B:323 , GLU B:329 , ASN B:341 , ASP B:342 , MAN B:405
BINDING SITE FOR RESIDUE CA B 401
07
AC7
SOFTWARE
HOH B:8 , ASP B:297 , GLU B:301 , ASP B:324 , GLU B:329 , ASP B:330
BINDING SITE FOR RESIDUE CA B 402
08
AC8
SOFTWARE
HOH B:165 , HOH B:169 , GLU B:301 , ASP B:330
BINDING SITE FOR RESIDUE CA B 403
09
AC9
SOFTWARE
GLU B:321 , ASN B:323 , ASP B:325 , GLU B:329 , ASN B:341 , ASP B:342 , ARG B:343 , CA B:401
BINDING SITE FOR RESIDUE MAN B 405
10
BC1
SOFTWARE
GLU C:321 , ASN C:323 , GLU C:329 , ASN C:341 , ASP C:342 , MAN C:405
BINDING SITE FOR RESIDUE CA C 401
11
BC2
SOFTWARE
HOH C:158 , ASP C:297 , GLU C:301 , ASP C:324 , GLU C:329 , ASP C:330
BINDING SITE FOR RESIDUE CA C 402
12
BC3
SOFTWARE
HOH C:23 , HOH C:166 , HOH C:167 , HOH C:168 , GLU C:301 , ASP C:330
BINDING SITE FOR RESIDUE CA C 403
13
BC4
SOFTWARE
GLU C:321 , ASN C:323 , GLU C:329 , ASN C:341 , ASP C:342 , ARG C:343 , CA C:401
BINDING SITE FOR RESIDUE MAN C 405
[
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SAPs(SNPs)/Variants
(2, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020940 (S270T, chain A/B/C, )
2: VAR_020941 (E289K, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020940
S
290
T
SFTPD_HUMAN
Polymorphism
3088308
A/B/C
S
270
T
2
UniProt
VAR_020941
E
309
K
SFTPD_HUMAN
Polymorphism
4469829
A/B/C
E
289
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: C_TYPE_LECTIN_2 (A:252-354,B:252-354,C:252-354)
2: C_TYPE_LECTIN_1 (A:331-353,B:331-353,C:331-353)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
C_TYPE_LECTIN_2
PS50041
C-type lectin domain profile.
SFTPD_HUMAN
272-374
3
A:252-354
B:252-354
C:252-354
2
C_TYPE_LECTIN_1
PS00615
C-type lectin domain signature.
SFTPD_HUMAN
351-373
3
A:331-353
B:331-353
C:331-353
[
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Exons
(2, 6)
Info
All Exons
Exon 1.8 (A:210-231 | B:210-231 | C:211-231)
Exon 1.9 (A:231-355 | B:231-355 | C:231-355)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.7b/1.8
2: Boundary 1.8/1.9
3: Boundary 1.9/-
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
1.2
ENST00000372292
2
ENSE00001457451
chr10:
81708859-81708822
38
SFTPD_HUMAN
-
0
0
-
-
1.3
ENST00000372292
3
ENSE00001679030
chr10:
81706418-81706217
202
SFTPD_HUMAN
1-67
67
0
-
-
1.4
ENST00000372292
4
ENSE00001388162
chr10:
81702635-81702519
117
SFTPD_HUMAN
67-106
40
0
-
-
1.5
ENST00000372292
5
ENSE00000909268
chr10:
81702260-81702144
117
SFTPD_HUMAN
106-145
40
0
-
-
1.6
ENST00000372292
6
ENSE00000909267
chr10:
81701826-81701710
117
SFTPD_HUMAN
145-184
40
0
-
-
1.7b
ENST00000372292
7b
ENSE00002173050
chr10:
81701270-81701154
117
SFTPD_HUMAN
184-223
40
0
-
-
1.8
ENST00000372292
8
ENSE00001708197
chr10:
81700544-81700461
84
SFTPD_HUMAN
223-251
29
3
A:210-231
B:210-231
C:211-231
22
22
21
1.9
ENST00000372292
9
ENSE00001920473
chr10:
81697984-81697496
489
SFTPD_HUMAN
251-375
125
3
A:231-355
B:231-355
C:231-355
125
125
125
[
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]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3ikqa2 (A:235-355)
1b: SCOP_d3ikqb2 (B:235-355)
1c: SCOP_d3ikqc2 (C:235-355)
2a: SCOP_d3ikqa1 (A:210-234)
2b: SCOP_d3ikqb1 (B:210-234)
2c: SCOP_d3ikqc1 (C:211-234)
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)
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Folds
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(
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
C-type lectin-like
(322)
Superfamily
:
C-type lectin-like
(322)
Family
:
C-type lectin domain
(182)
Protein domain
:
Surfactant protein, lectin domain
(16)
Human (Homo sapiens), SP-D [TaxId: 9606]
(9)
1a
d3ikqa2
A:235-355
1b
d3ikqb2
B:235-355
1c
d3ikqc2
C:235-355
Class
:
Coiled coil proteins
(689)
Fold
:
Parallel coiled-coil
(407)
Superfamily
:
Triple coiled coil domain of C-type lectins
(54)
Family
:
Triple coiled coil domain of C-type lectins
(54)
Protein domain
:
Surfactant protein
(30)
Human (Homo sapiens), SP-D [TaxId: 9606]
(24)
2a
d3ikqa1
A:210-234
2b
d3ikqb1
B:210-234
2c
d3ikqc1
C:211-234
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_3ikqC00 (C:211-355)
1b: CATH_3ikqA00 (A:210-355)
1c: CATH_3ikqB00 (B:210-355)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Mannose-Binding Protein A; Chain A
(180)
Homologous Superfamily
:
Mannose-Binding Protein A, subunit A
(180)
Human (Homo sapiens)
(80)
1a
3ikqC00
C:211-355
1b
3ikqA00
A:210-355
1c
3ikqB00
B:210-355
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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