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1PWB
Asym. Unit
Info
Asym.Unit (88 KB)
Biol.Unit 1 (82 KB)
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(1)
Title
:
HIGH RESOLUTION CRYSTAL STRUCTURE OF AN ACTIVE RECOMBINANT FRAGMENT OF HUMAN LUNG SURFACTANT PROTEIN D WITH MALTOSE
Authors
:
A. K. Shrive, H. A. Tharia, P. Strong, U. Kishore, I. Burns, P. J. Rizkallah, K. B. Reid, T. J. Greenhough
Date
:
01 Jul 03 (Deposition) - 05 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Collectin, C-Type Lectin, Alpha-Helical Coiled Coil, Carbohydrate Recognition Domain, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. K. Shrive, H. A. Tharia, P. Strong, U. Kishore, I. Burns, P. J. Rizkallah, K. B. Reid, T. J. Greenhough
High-Resolution Structural Insights Into Ligand Binding And Immune Cell Recognition By Human Lung Surfactant Protein D
J. Mol. Biol. V. 331 509 2003
(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)
2a: ALPHA-D-GLUCOSE (GLCa)
2b: ALPHA-D-GLUCOSE (GLCb)
2c: ALPHA-D-GLUCOSE (GLCc)
2d: ALPHA-D-GLUCOSE (GLCd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
9
Ligand/Ion
CALCIUM ION
2
GLC
4
Ligand/Ion
ALPHA-D-GLUCOSE
[
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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 , ARG A:343 , CA A:401 , GLC A:406 , HOH A:521 , HOH A:537
BINDING SITE FOR RESIDUE GLC A 405
02
AC2
SOFTWARE
ARG A:343 , GLC A:405 , HOH A:473
BINDING SITE FOR RESIDUE GLC A 406
03
AC3
SOFTWARE
GLU B:321 , ASN B:323 , GLU B:329 , ASN B:341 , ASP B:342 , ARG B:343 , CA B:401
BINDING SITE FOR RESIDUE GLC B 405
04
AC4
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 GLC C 405
05
AC5
SOFTWARE
GLU A:321 , ASN A:323 , GLU A:329 , ASN A:341 , ASP A:342 , GLC A:405
BINDING SITE FOR RESIDUE CA A 401
06
AC6
SOFTWARE
ASP A:297 , GLU A:301 , ASP A:324 , GLU A:329 , ASP A:330 , HOH A:411
BINDING SITE FOR RESIDUE CA A 402
07
AC7
SOFTWARE
GLU A:301 , ASP A:330 , HOH A:417 , HOH A:461 , HOH A:475 , HOH A:564
BINDING SITE FOR RESIDUE CA A 403
08
AC8
SOFTWARE
GLU B:321 , ASN B:323 , GLU B:329 , ASN B:341 , ASP B:342 , GLC B:405
BINDING SITE FOR RESIDUE CA B 401
09
AC9
SOFTWARE
ASP B:297 , GLU B:301 , ASP B:324 , GLU B:329 , ASP B:330 , HOH B:409
BINDING SITE FOR RESIDUE CA B 402
10
BC1
SOFTWARE
GLU B:301 , ASP B:330 , HOH B:417 , HOH B:420 , HOH B:429 , HOH B:501
BINDING SITE FOR RESIDUE CA B 403
11
BC2
SOFTWARE
GLU C:321 , ASN C:323 , GLU C:329 , ASN C:341 , ASP C:342 , GLC C:405
BINDING SITE FOR RESIDUE CA C 401
12
BC3
SOFTWARE
ASP C:297 , GLU C:301 , ASP C:324 , GLU C:329 , ASP C:330 , HOH C:406
BINDING SITE FOR RESIDUE CA C 402
13
BC4
SOFTWARE
GLU C:301 , ASP C:330 , HOH C:417 , HOH C:418 , HOH C:441 , HOH C:489
BINDING SITE FOR RESIDUE CA C 403
[
close Site info
]
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:
Select:
Label:
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
[
close PROSITE info
]
Exons
(2, 6)
Info
All Exons
Exon 1.8 (A:205-231 | B:205-231 | C:206-231)
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:205-231
B:205-231
C:206-231
27
27
26
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
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1pwba1 (A:235-355)
1b: SCOP_d1pwbb1 (B:235-355)
1c: SCOP_d1pwbc1 (C:235-355)
2a: SCOP_d1pwba2 (A:205-234)
2b: SCOP_d1pwbb2 (B:205-234)
2c: SCOP_d1pwbc2 (C:206-234)
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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
d1pwba1
A:235-355
1b
d1pwbb1
B:235-355
1c
d1pwbc1
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
d1pwba2
A:205-234
2b
d1pwbb2
B:205-234
2c
d1pwbc2
C:206-234
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1pwbC00 (C:206-355)
1b: CATH_1pwbA00 (A:205-355)
1c: CATH_1pwbB00 (B:205-355)
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(
)
(
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Architectures
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)
(
)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
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
1pwbC00
C:206-355
1b
1pwbA00
A:205-355
1c
1pwbB00
B:205-355
[
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]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Lectin_C_1pwbC01 (C:251-355)
1b: PFAM_Lectin_C_1pwbC02 (C:251-355)
1c: PFAM_Lectin_C_1pwbC03 (C:251-355)
2a: PFAM_Surfac_D_trimer_1pwbC04 (C:206-249)
2b: PFAM_Surfac_D_trimer_1pwbC05 (C:206-249)
2c: PFAM_Surfac_D_trimer_1pwbC06 (C:206-249)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
C_Lectin
(98)
Family
:
Lectin_C
(85)
Homo sapiens (Human)
(39)
1a
Lectin_C-1pwbC01
C:251-355
1b
Lectin_C-1pwbC02
C:251-355
1c
Lectin_C-1pwbC03
C:251-355
Clan
:
no clan defined [family: Surfac_D-trimer]
(9)
Family
:
Surfac_D-trimer
(9)
Homo sapiens (Human)
(9)
2a
Surfac_D-trimer-1pwbC04
C:206-249
2b
Surfac_D-trimer-1pwbC05
C:206-249
2c
Surfac_D-trimer-1pwbC06
C:206-249
[
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Protein & NOT PROSITE
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Chain C
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Asym.Unit (88 KB)
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