3T9G - JenaLib

Asymmetric Unit (9, 25)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	CL	1	Ligand/Ion	CHLORIDE ION
4	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
5	GOL	4	Ligand/Ion	GLYCEROL
6	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
7	MRD	4	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
8	NA	4	Ligand/Ion	SODIUM ION
9	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
5	GOL	2	Ligand/Ion	GLYCEROL
6	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
7	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
8	NA	-1	Ligand/Ion	SODIUM ION
9	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (6, 12)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
5	GOL	2	Ligand/Ion	GLYCEROL
6	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
7	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
8	NA	-1	Ligand/Ion	SODIUM ION
9	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (6, 12)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
5	GOL	2	Ligand/Ion	GLYCEROL
6	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
7	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
8	NA	-1	Ligand/Ion	SODIUM ION
9	PO4	2	Ligand/Ion	PHOSPHATE ION

Sites (25, 25)

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:81 , VAL A:82 , GLU A:104 , HOH A:316 , HOH A:352 , HOH A:361 , HOH A:400	BINDING SITE FOR RESIDUE CA A 201
02	AC2	SOFTWARE	LEU A:6 , ILE A:8 , ILE A:12 , TYR A:20 , HOH A:408 , THR B:0 , ASN B:1 , GLY B:4	BINDING SITE FOR RESIDUE MRD A 202
03	AC3	SOFTWARE	LEU A:6 , HOH A:490 , HOH A:493 , HOH A:558 , HOH A:567 , ASN B:1 , TYR B:20	BINDING SITE FOR RESIDUE MRD A 203
04	AC4	SOFTWARE	LYS A:119 , TYR A:145 , GLU A:147 , PRO A:164 , SER A:186 , TYR A:193 , HOH A:560 , HOH A:568	BINDING SITE FOR RESIDUE MPD A 204
05	AC5	SOFTWARE	GLU A:92 , GLY A:93 , PRO A:115 , CYS A:116 , THR A:117 , LYS A:141 , VAL A:143 , HOH A:317 , HOH A:436 , HOH A:496 , HOH A:554 , HOH A:572 , HOH A:573	BINDING SITE FOR RESIDUE MPD A 205
06	AC6	SOFTWARE	ASP A:64 , GLU A:84 , ASP A:85 , HOH A:374 , HOH A:398	BINDING SITE FOR RESIDUE NA A 206
07	AC7	SOFTWARE	LYS A:108 , LYS A:130 , ARG A:133 , LYS A:160 , HOH A:349 , HOH A:555 , HOH A:569	BINDING SITE FOR RESIDUE GOL A 207
08	AC8	SOFTWARE	ASN A:153 , VAL A:154 , LYS A:155 , ASN A:177 , HOH A:506 , HOH A:564	BINDING SITE FOR RESIDUE GOL A 208
09	AC9	SOFTWARE	ASP B:81 , VAL B:82 , GLU B:104 , HOH B:303 , HOH B:331 , HOH B:353 , HOH B:360	BINDING SITE FOR RESIDUE CA B 201
10	BC1	SOFTWARE	GLU B:39 , LYS B:90 , ASN B:113	BINDING SITE FOR RESIDUE CL B 202
11	BC2	SOFTWARE	ASN A:137 , THR A:139 , HOH A:335 , HOH A:532 , ASP B:148 , ASN B:172	BINDING SITE FOR RESIDUE MRD B 203
12	BC3	SOFTWARE	ASN A:137 , GLN A:192 , HOH A:335 , HOH A:518 , HOH A:532 , LYS B:121 , ASP B:148	BINDING SITE FOR RESIDUE MPD B 204
13	BC4	SOFTWARE	THR A:0 , ASN A:1 , GLY A:4 , LEU B:6 , ILE B:12 , TYR B:20 , HOH B:317	BINDING SITE FOR RESIDUE MPD B 205
14	BC5	SOFTWARE	LYS B:108 , LYS B:130 , ARG B:133 , LYS B:160 , ACT B:215 , HOH B:359 , HOH B:398 , HOH B:409 , HOH B:478 , HOH B:540 , HOH B:541 , HOH B:542	BINDING SITE FOR RESIDUE MRD B 206
15	BC6	SOFTWARE	GLU B:147 , TYR B:193 , HOH B:529	BINDING SITE FOR RESIDUE EDO B 207
16	BC7	SOFTWARE	PHE B:182 , PHE B:184 , GLN B:187 , HOH B:387 , HOH B:533	BINDING SITE FOR RESIDUE EDO B 208
17	BC8	SOFTWARE	ASP B:64 , GLU B:84 , ASP B:85 , HOH B:364 , HOH B:431	BINDING SITE FOR RESIDUE NA B 209
18	BC9	SOFTWARE	GLN B:37 , ASP B:107 , ASN B:135 , GLY B:136 , HOH B:323 , HOH B:398 , HOH B:482 , HOH B:483	BINDING SITE FOR RESIDUE NA B 210
19	CC1	SOFTWARE	SER B:36 , GLN B:37 , HOH B:342 , HOH B:347 , HOH B:550	BINDING SITE FOR RESIDUE NA B 211
20	CC2	SOFTWARE	ALA B:102 , LYS B:103 , THR B:124 , ALA B:125 , THR B:126	BINDING SITE FOR RESIDUE GOL B 212
21	CC3	SOFTWARE	ASN B:52 , LYS B:54 , GLU B:75	BINDING SITE FOR RESIDUE GOL B 213
22	CC4	SOFTWARE	GLN A:30 , HOH B:517 , HOH B:538	BINDING SITE FOR RESIDUE ACT B 214
23	CC5	SOFTWARE	GLU B:39 , LYS B:108 , MRD B:206 , HOH B:398 , HOH B:482 , HOH B:483	BINDING SITE FOR RESIDUE ACT B 215
24	CC6	SOFTWARE	PRO B:115 , CYS B:116 , LYS B:141 , HOH B:372 , HOH B:394 , HOH B:534 , HOH B:543	BINDING SITE FOR RESIDUE PO4 B 216
25	CC7	SOFTWARE	ASP B:71 , VAL B:94 , GLU B:96 , HOH B:523 , HOH B:544 , HOH B:545	BINDING SITE FOR RESIDUE PO4 B 217

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:196
 aligned with B9MKT4_CALBD | B9MKT4 from UniProtKB/TrEMBL  Length:460

    Alignment length:207
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       
         B9MKT4_CALBD   254 VPTQTPAVTPTPTPNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 460
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-----------....eeee...eee....eeeeeeeeeee...............eee....eeeeeee.......eee...eeeeeeee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t9g A  -2 VGT-----------NTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                              |      -    |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       
                              0           1

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with B9MKT4_CALBD | B9MKT4 from UniProtKB/TrEMBL  Length:460

    Alignment length:195
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455     
         B9MKT4_CALBD   266 TPNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 460
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eee....eeeeeeeeeee...............eee....eeeeeee.......eee...eeeeeeee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee........eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t9g B  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (B9MKT4_CALBD | B9MKT4)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030570	pectate lyase activity	Catalysis of the reaction: a pectate = a pectate + a pectate oligosaccharide with 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate end. This reaction is the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
cellular component
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Cis Peptide Bonds
		Ala A:60 - Pro A:61	[ RasMol ]
		Ala B:60 - Pro B:61	[ RasMol ]

Biological Units
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	3t9g
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	B9MKT4_CALBD \| B9MKT4
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	4.2.2.2
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 25)