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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3WN6

Crystal structure of alpha-amylase AmyI-1 from Oryza sativa

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004556	molecular_function	alpha-amylase activity
A	0005509	molecular_function	calcium ion binding
A	0005975	biological_process	carbohydrate metabolic process
A	0043169	molecular_function	cation binding
B	0004556	molecular_function	alpha-amylase activity
B	0005509	molecular_function	calcium ion binding
B	0005975	biological_process	carbohydrate metabolic process
B	0043169	molecular_function	cation binding
C	0004556	molecular_function	alpha-amylase activity
C	0005509	molecular_function	calcium ion binding
C	0005975	biological_process	carbohydrate metabolic process
C	0043169	molecular_function	cation binding
D	0004556	molecular_function	alpha-amylase activity
D	0005509	molecular_function	calcium ion binding
D	0005975	biological_process	carbohydrate metabolic process
D	0043169	molecular_function	cation binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 501

Chain	Residue
A	GLU133
A	THR136
A	ASP138
A	ASP142
A	HOH624
A	HOH750

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 502

Chain	Residue
A	ALA170
A	ASP172
A	HOH629
A	ASP152
A	ASP166
A	PHE167

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA A 503

Chain	Residue
A	ASN116
A	ASP162
A	ALA165
A	ASP172
A	GLY207
A	HOH683

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 504

Chain	Residue
A	TRP34
A	GLN74
A	TYR76
A	MET77
A	HOH614
A	HOH723

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 505

Chain	Residue
A	ASP203
A	HIS313
A	ASP314
A	HOH603
A	HOH604

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE TAR A 506

Chain	Residue
A	GLN250
A	TRP301
A	TAR507
A	HOH607
A	HOH788

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE TAR A 507

Chain	Residue
A	TRP301
A	TRP302
A	TAR506
A	HOH605
A	HOH606

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG A 508

Chain	Residue
A	THR60
A	GLY106
A	GLN108
A	HOH901
A	HOH959
D	HIS320

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PEG A 509

Chain	Residue
A	LYS240
A	ASN278
A	PRO323
A	HOH694
D	GLU100
D	ALA101
D	GLY104
D	HOH681

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 501

Chain	Residue
B	ASN116
B	ASP162
B	ALA165
B	ASP172
B	GLY207
B	HOH667

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 502

Chain	Residue
B	GLU133
B	THR136
B	ASP138
B	ASP142
B	HOH644
B	HOH710

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA B 503

Chain	Residue
B	ASP152
B	ASP166
B	PHE167
B	ALA170
B	ASP172
B	HOH654

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL B 504

Chain	Residue
B	HOH605
B	HOH861
B	HOH934

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 505

Chain	Residue
B	ASP314
B	HOH601
B	HOH602
B	HOH603
B	HOH797

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 506

Chain	Residue
B	ASP142
B	TRP143
B	GLY144
B	ARG179
B	HOH736
B	HOH771
B	HOH821
B	HOH866

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE TAR B 507

Chain	Residue
B	TRP301
B	HOH827
B	HOH828
B	HOH829
B	HOH830
B	HOH857

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG B 508

Chain	Residue
B	TRP286
B	HOH981
B	HOH983

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA C 501

Chain	Residue
C	ASP172
C	GLY207
C	HOH674
C	ASN116
C	ASP162
C	ALA165

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA C 502

Chain	Residue
C	GLU133
C	THR136
C	ASP138
C	ASP142
C	HOH614
C	HOH646

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA C 503

Chain	Residue
C	ASP152
C	ASP166
C	PHE167
C	ALA170
C	ASP172
C	HOH610

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 504

Chain	Residue
C	HIS313
C	ASP314
C	HOH601
C	HOH602
C	HOH634

site_id	CC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL C 505

Chain	Residue
C	HIS418
C	HOH652

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE TAR C 506

Chain	Residue
C	GLN250
C	TRP301
C	TAR507
C	HOH603
C	HOH852

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE TAR C 507

Chain	Residue
C	VAL253
C	TRP302
C	TAR506
C	HOH973

site_id	CC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA D 501

Chain	Residue
D	ASN116
D	ASP162
D	ALA165
D	ASP172
D	GLY207
D	HOH663

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA D 502

Chain	Residue
D	GLU133
D	THR136
D	ASP138
D	ASP142
D	HOH649
D	HOH683

site_id	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CA D 503

Chain	Residue
D	ASP152
D	ASP166
D	PHE167
D	ALA170
D	ASP172
D	HOH660

site_id	DC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL D 504

Chain	Residue
D	TRP230
D	HOH604

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 505

Chain	Residue
D	PHE167
D	HOH602
D	HOH603
D	HOH698
D	HOH921

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE TAR D 506

Chain	Residue
C	ASP238
D	TRP302
D	HOH872
D	HOH886
D	HOH948
D	HOH953

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PEG D 507

Chain	Residue
D	GLU282
D	GLY283
D	HOH688

site_id	DC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PEG D 508

Chain	Residue
D	THR163
D	GLY164
D	ALA205
D	LYS206
D	TYR208
D	SER209
D	ALA210
D	TRP255
D	HOH751
D	HOH828

site_id	DC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PEG D 509

Chain	Residue
D	TRP286
D	HOH985

site_id	DC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG D 510

Chain	Residue
D	ARG150
D	ASP151
D	ASP152
D	GLY155
D	HOH981
D	HOH1009

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"UniProtKB","id":"P00693","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"P00693","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	156
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P00693","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P04063","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Site: {"description":"Transition state stabilizer","evidences":[{"source":"UniProtKB","id":"P00693","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

247536

PDB entries from 2026-01-14

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