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Title :   CRYSTAL STRUCTURE OF THE TRIMERIC NECK AND CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN SURFACTANT PROTEIN D IN COMPLEX WITH MALTOTRIOSE

Authors :   J. F. Head

Date :   24 Mar 06 (Deposition) - 02 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Protein-Carbohydrate Ligand Complex, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Crouch, B. Mcdonald, K. Smith, T. Cafarella, B. Seaton, J. Head
Contributions Of Phenylalanine 335 To Ligand Recognition By Human Surfactant Protein D: Ring Interactions With Sp-D Ligands
J. Biol. Chem. V. 281 18008 2006
PubMed-ID: 16636058 | Reference-DOI: 10.1074/JBC.M601749200
(for further references see the PDB file header)

Molecule 1 - PULMONARY SURFACTANT-ASSOCIATED PROTEIN D
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	TRIMERIC NECK AND CARBOHYDRATE RECOGNITION DOMAIN
	Gene	:	SFTPD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SP-D, PSP-D

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	CA	9	Ligand/Ion	CALCIUM ION
2	MLR	3	Ligand/Ion	MALTOTRIOSE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:321 , ASN A:323 , GLU A:329 , ASN A:341 , ASP A:342 , MLR A:3505	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 , HOH A:3600	BINDING SITE FOR RESIDUE CA A 402
03	AC3	SOFTWARE	GLU A:301 , ASP A:330 , HOH A:3525 , HOH A:3598 , HOH A:3601 , HOH A:3602	BINDING SITE FOR RESIDUE CA A 403
04	AC4	SOFTWARE	GLU B:321 , ASN B:323 , GLU B:329 , ASN B:341 , ASP B:342 , MLR B:3505	BINDING SITE FOR RESIDUE CA B 401
05	AC5	SOFTWARE	ASP B:297 , GLU B:301 , ASP B:324 , GLU B:329 , ASP B:330 , HOH B:3597	BINDING SITE FOR RESIDUE CA B 402
06	AC6	SOFTWARE	GLU B:301 , ASP B:330 , HOH B:3601 , HOH B:3602 , HOH B:3603 , HOH B:3604	BINDING SITE FOR RESIDUE CA B 403
07	AC7	SOFTWARE	GLU C:321 , ASN C:323 , GLU C:329 , ASN C:341 , ASP C:342 , MLR C:3505	BINDING SITE FOR RESIDUE CA C 401
08	AC8	SOFTWARE	ASP C:297 , GLU C:301 , ASP C:324 , GLU C:329 , ASP C:330 , HOH C:3583	BINDING SITE FOR RESIDUE CA C 402
09	AC9	SOFTWARE	GLU C:301 , ASP C:330 , HOH C:3575 , HOH C:3577 , HOH C:3581	BINDING SITE FOR RESIDUE CA C 403
10	BC1	SOFTWARE	GLU A:321 , ASN A:323 , GLU A:329 , PHE A:335 , THR A:336 , ASN A:337 , ASN A:341 , ASP A:342 , ARG A:343 , CA A:401 , HOH A:3568	BINDING SITE FOR RESIDUE MLR A 3505
11	BC2	SOFTWARE	GLU B:321 , ASN B:323 , GLU B:329 , PHE B:335 , THR B:336 , ASN B:337 , ASN B:341 , ASP B:342 , ARG B:343 , CA B:401 , HOH B:3523 , HOH B:3525	BINDING SITE FOR RESIDUE MLR B 3505
12	BC3	SOFTWARE	GLU C:321 , ASN C:323 , GLU C:329 , PHE C:335 , THR C:336 , ASN C:337 , ASN C:341 , ASP C:342 , ARG C:343 , CA C:401 , HOH C:3522 , HOH C:3531	BINDING SITE FOR RESIDUE MLR C 3505

Asymmetric/Biological Unit

No.	Residues
1	A:261	-	A:353
2	A:331	-	A:345
3	B:261	-	B:353
4	B:331	-	B:345
5	C:261	-	C:353
6	C:331	-	C:345

Asymmetric/Biological Unit

No.	Residues
1	Phe A:234	-	Pro A:235
2	Glu A:321	-	Pro A:322
3	Phe B:234	-	Pro B:235
4	Glu B:321	-	Pro B:322
5	Phe C:234	-	Pro C:235
6	Glu C:321	-	Pro C:322

Asymmetric/Biological Unit (2, 6)

								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)

Asymmetric/Biological Unit (2, 6)

	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

Asymmetric/Biological Unit (2, 6)

	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:205-231	27 27 27
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

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:151
 aligned with SFTPD_HUMAN | P35247 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:151
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374 
          SFTPD_HUMAN   225 ASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF 375
               SCOP domains d2ggua2 A:205-234             d2ggua1 A:235-355 Surfactant protein, lectin domain                                                                       SCOP domains
               CATH domains 2gguA00 A:205-355 Mannose-Binding Protein A, subunit A                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeeeeeehhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh..ee...............................hhhhh..eeee.....eeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------T------------------K------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------------------------C_TYPE_LECTIN_2  PDB: A:252-354 UniProt: 272-374                                                       - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        -- PROSITE (2)
           Transcript 1 (1) Exon 1.8  PDB: A:205-231   ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.9  PDB: A:231-355 UniProt: 251-375                                                                                     Transcript 1 (2)
                 2ggu A 205 ASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF 355
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with SFTPD_HUMAN | P35247 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:151
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374 
          SFTPD_HUMAN   225 ASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF 375
               SCOP domains d2ggub2 B:205-234             d2ggub1 B:235-355 Surfactant protein, lectin domain                                                                       SCOP domains
               CATH domains 2gguB00 B:205-355 Mannose-Binding Protein A, subunit A                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeeeeeehhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh..ee...............................hhhhh..eeee.....eeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------T------------------K------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------------------------C_TYPE_LECTIN_2  PDB: B:252-354 UniProt: 272-374                                                       - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        -- PROSITE (2)
           Transcript 1 (1) Exon 1.8  PDB: B:205-231   ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.9  PDB: B:231-355 UniProt: 251-375                                                                                     Transcript 1 (2)
                 2ggu B 205 ASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF 355
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with SFTPD_HUMAN | P35247 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:151
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374 
          SFTPD_HUMAN   225 ASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF 375
               SCOP domains d2gguc2 C:205-234             d2gguc1 C:235-355 Surfactant protein, lectin domain                                                                       SCOP domains
               CATH domains 2gguC00 C:205-355 Mannose-Binding Protein A, subunit A                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh..ee...............................hhhhh..eeee.....eeee.....eeeeeee Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------T------------------K------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------------------------C_TYPE_LECTIN_2  PDB: C:252-354 UniProt: 272-374                                                       - PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        -- PROSITE (2)
           Transcript 1 (1) Exon 1.8  PDB: C:205-231   ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.9  PDB: C:231-355 UniProt: 251-375                                                                                     Transcript 1 (2)
                 2ggu C 205 ASLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTEAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTYPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF 355
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

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	d2ggua1	A:235-355
1b	d2ggub1	B:235-355
1c	d2gguc1	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	d2ggua2	A:205-234
2b	d2ggub2	B:205-234
2c	d2gguc2	C:205-234

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	2gguA00	A:205-355
1b	2gguB00	B:205-355
1c	2gguC00	C:205-355

(no "Pfam Domain" information available for 2GGU)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (SFTPD_HUMAN | P35247)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0048286	lung alveolus development	The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways.
	GO:0048246	macrophage chemotaxis	The movement of a macrophage in response to an external stimulus.
	GO:0042130	negative regulation of T cell proliferation	Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
	GO:0045085	negative regulation of interleukin-2 biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
	GO:0050766	positive regulation of phagocytosis	Any process that activates or increases the frequency, rate or extent of phagocytosis.
	GO:0072593	reactive oxygen species metabolic process	The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0001817	regulation of cytokine production	Any process that modulates the frequency, rate, or extent of production of a cytokine.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0007585	respiratory gaseous exchange	The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
	GO:0043129	surfactant homeostasis	Any process involved in the maintenance of a steady-state level of the surface-active lipoprotein mixture which coats the alveoli.
cellular component
	GO:0045334	clathrin-coated endocytic vesicle	A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance.
	GO:0005581	collagen trimer	A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0042599	lamellar body	A membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:321 - Pro A:322	[ RasMol ]
		Glu B:321 - Pro B:322	[ RasMol ]
		Glu C:321 - Pro C:322	[ RasMol ]
		Phe A:234 - Pro A:235	[ RasMol ]
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		Phe C:234 - Pro C:235	[ RasMol ]

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	2ggu
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 6)

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Exons (2, 6)

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SCOP Domains (2, 6)

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Gene Ontology (27, 27)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File