1RIN - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION

Authors :   J. M. Rini, K. D. Hardman, H. Einspahr, F. L. Suddath, J. P. Carver

Date :   27 Jan 93 (Deposition) - 31 Oct 93 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: C,D  (1x)

Keywords :   Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Rini, K. D. Hardman, H. Einspahr, F. L. Suddath, J. P. Carver
X-Ray Crystal Structure Of A Pea Lectin-Trimannoside Comple At 2. 6 A Resolution.
J. Biol. Chem. V. 268 10126 1993
PubMed-ID: 8486683
(for further references see the PDB file header)

Molecule 1 - PEA LECTIN
	Chains	:	A, C
	Engineered	:	YES
	Organism Common	:	PEA
	Organism Scientific	:	PISUM SATIVUM
	Organism Taxid	:	3888

Molecule 2 - PEA LECTIN
	Chains	:	B, D
	Engineered	:	YES
	Organism Common	:	PEA
	Organism Scientific	:	PISUM SATIVUM
	Organism Taxid	:	3888

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
3	MN	2	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:80 , ASP A:81 , GLY A:99 , PHE A:123 , ASN A:125 , GLY B:216 , ALA B:217 , GLU B:218	BINDING SITE FOR RESIDUE MAN A 250
2	AC2	SOFTWARE	ALA C:80 , ASP C:81 , GLY C:99 , PHE C:123 , ASN C:125 , GLY D:216 , ALA D:217 , GLU D:218	BINDING SITE FOR RESIDUE MAN C 250
3	AC3	SOFTWARE	GLU A:119 , ASP A:121 , ASP A:129 , HIS A:136 , HOH A:251 , HOH A:252	BINDING SITE FOR RESIDUE MN A 240
4	AC4	SOFTWARE	ASP A:121 , PHE A:123 , ASN A:125 , ASP A:129 , HOH A:253 , HOH A:254	BINDING SITE FOR RESIDUE CA A 243
5	AC5	SOFTWARE	GLU C:119 , ASP C:121 , ASP C:129 , HIS C:136 , HOH C:341 , HOH C:342	BINDING SITE FOR RESIDUE MN C 240
6	AC6	SOFTWARE	ASP C:121 , PHE C:123 , ASN C:125 , ASP C:129 , HOH C:343 , HOH C:344	BINDING SITE FOR RESIDUE CA C 243

(no "SS Bond" information available for 1RIN)

Asymmetric Unit

No.	Residues
1	Ala A:80	-	Asp A:81
2	Ala C:80	-	Asp C:81

(no "SAP(SNP)/Variant" information available for 1RIN)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LEC_PEA	146-152	2	A:116-122 C:116-122
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC_PEA	233-242	2	B:203-212 D:203-212

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LEC_PEA	146-152	2	A:116-122 C:116-122
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC_PEA	233-242	2	B:203-212 D:203-212

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LEC_PEA	146-152	1	A:116-122 -
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC_PEA	233-242	1	B:203-212 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LEC_PEA	146-152	1	- C:116-122
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LEC_PEA	233-242	1	- D:203-212

(no "Exon" information available for 1RIN)

Asymmetric 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:180
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:180
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
              LEC_PEA    31 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYP 210
               SCOP domains d1rin.1 A:,B: Legume lectin                                                                                                                                                          SCOP domains
               CATH domains 1rinA00 A:1-180  [code=2.60.120.200, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeee..................eeeeee...ee..............................eeeeeeee.......hhhhh........hhhhh.eeeeee..............eeeeee......eeee............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rin A   1 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTETVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYP 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:47
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:47
                                   227       237       247       257       
              LEC_PEA   218 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 264
               SCOP domains d1rin.1 A:,B: Legume lectin                     SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh..eeeeeeeee.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG---------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 1rin B 188 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELS 234
                                   197       207       217       227

Chain C from PDB  Type:PROTEIN  Length:180
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:180
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
              LEC_PEA    31 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTQTVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYP 210
               SCOP domains d1rin.2 C:,D: Legume lectin                                                                                                                                                          SCOP domains
               CATH domains 1rinC00 C:1-180  [code=2.60.120.200, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeee..................eeeeee...ee..............................eeeeeee........hhhhh..............eeeeee..............eeeeee......eeee............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rin C   1 TETTSFLITKFSPDQQNLIFQGDGYTTKEKLTLTKAVKNTVGRALYSSPIHIWDRETGNVANFVTSFTFVINAPNSYNVADGFTFFIAPVDTKPQTGGGYLGVFNSAEYDKTTETVAVEFDTFYNAAWDPSNRDRHIGIDVNSIKSVNTKSWKLQNGEEANVVIAFNAATNVLTVSLTYP 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain D from PDB  Type:PROTEIN  Length:49
 aligned with LEC_PEA | P02867 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:49
                                   227       237       247       257         
              LEC_PEA   218 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT 266
               SCOP domains d1rin.2 C:,D: Legume lectin                       SCOP domains
               CATH domains ------------------------------------------------- CATH domains
           Pfam domains (1) Lectin_legB-1rinD01 D:188-230              ------ Pfam domains (1)
           Pfam domains (2) Lectin_legB-1rinD02 D:188-230              ------ Pfam domains (2)
           Pfam domains (3) Lectin_legB-1rinD03 D:188-230              ------ Pfam domains (3)
           Pfam domains (4) Lectin_legB-1rinD04 D:188-230              ------ Pfam domains (4)
         Sec.struct. author ..........hhhhhh..eeeeeeeee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG------------------------ PROSITE
                 Transcript ------------------------------------------------- Transcript
                 1rin D 188 VTSYTLSDVVSLKDVVPEWVRIGFSATTGAEYAAHEVLSWSFHSELSGT 236
                                   197       207       217       227

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Legume lectins (238)

Protein domain: Legume lectin (110)

Pea (Pisum sativum) [TaxId: 3888] (6)

1a	d1rin.1	A:,B:
1b	d1rin.2	C:,D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Pea (Pisum sativum) (4)

1a	1rinA00	A:1-180
1b	1rinC00	C:1-180

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Lectin_legB (93)

Pisum sativum (Garden pea) (3)

1a	Lectin_legB-1rinD01	D:188-230
1b	Lectin_legB-1rinD02	D:188-230
1c	Lectin_legB-1rinD03	D:188-230
1d	Lectin_legB-1rinD04	D:188-230

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LEC_PEA | P02867)


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:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:80 - Asp A:81	[ RasMol ]
		Ala C:80 - Asp C:81	[ RasMol ]

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	LEC_PEA \| P02867	:	1bqp 1hkd 1ofs 2bqp 2ltn

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Description

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Ligands, Modified Residues, Ions (3, 6)

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