Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6TLK

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004488	molecular_function	methylenetetrahydrofolate dehydrogenase (NADP+) activity
A	0005737	cellular_component	cytoplasm
A	0006730	biological_process	one-carbon metabolic process
A	0016491	molecular_function	oxidoreductase activity
A	0046294	biological_process	formaldehyde catabolic process
B	0004488	molecular_function	methylenetetrahydrofolate dehydrogenase (NADP+) activity
B	0005737	cellular_component	cytoplasm
B	0006730	biological_process	one-carbon metabolic process
B	0016491	molecular_function	oxidoreductase activity
B	0046294	biological_process	formaldehyde catabolic process
C	0004488	molecular_function	methylenetetrahydrofolate dehydrogenase (NADP+) activity
C	0005737	cellular_component	cytoplasm
C	0006730	biological_process	one-carbon metabolic process
C	0016491	molecular_function	oxidoreductase activity
C	0046294	biological_process	formaldehyde catabolic process
D	0004488	molecular_function	methylenetetrahydrofolate dehydrogenase (NADP+) activity
D	0005737	cellular_component	cytoplasm
D	0006730	biological_process	one-carbon metabolic process
D	0016491	molecular_function	oxidoreductase activity
D	0046294	biological_process	formaldehyde catabolic process
E	0004488	molecular_function	methylenetetrahydrofolate dehydrogenase (NADP+) activity
E	0005737	cellular_component	cytoplasm
E	0006730	biological_process	one-carbon metabolic process
E	0016491	molecular_function	oxidoreductase activity
E	0046294	biological_process	formaldehyde catabolic process
F	0004488	molecular_function	methylenetetrahydrofolate dehydrogenase (NADP+) activity
F	0005737	cellular_component	cytoplasm
F	0006730	biological_process	one-carbon metabolic process
F	0016491	molecular_function	oxidoreductase activity
F	0046294	biological_process	formaldehyde catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	33
Details	binding site for residue NAP A 401

Chain	Residue
A	ASN97
A	LYS156
A	ALA196
A	GLY197
A	ALA198
A	ILE199
A	LEU201
A	TYR221
A	ASN222
A	LYS256
A	H4M404
A	THR102
A	HOH508
A	HOH548
A	HOH578
A	HOH595
A	HOH598
A	HOH599
A	HOH600
A	HOH601
A	HOH657
A	HOH663
A	ALA127
A	HOH692
A	HOH701
A	HOH706
A	HOH719
A	THR129
A	GLY130
A	PRO131
A	VAL132
A	GLY151
A	ARG152

site_id	AC2
Number of Residues	4
Details	binding site for residue FMT A 402

Chain	Residue
A	ARG167
A	HOH527
A	HOH675
A	HOH756

site_id	AC3
Number of Residues	4
Details	binding site for residue FMT A 403

Chain	Residue
A	PHE85
A	GLY86
A	HOH640
D	LYS153

site_id	AC4
Number of Residues	23
Details	binding site for residue H4M A 404

Chain	Residue
A	SER16
A	PHE18
A	ASP19
A	ASN97
A	GLY98
A	THR235
A	LEU250
A	GLY253
A	GLY254
A	LYS256
A	LEU257
A	NAP401
A	HOH512
A	HOH530
A	HOH577
A	HOH619
A	HOH621
A	HOH663
A	HOH671
A	HOH686
A	HOH733
C	TYR51
C	GOL403

site_id	AC5
Number of Residues	32
Details	binding site for residue NAP B 401

Chain	Residue
B	ASN97
B	THR102
B	ALA127
B	THR129
B	GLY130
B	PRO131
B	VAL132
B	GLY151
B	ARG152
B	LYS156
B	ALA196
B	GLY197
B	ALA198
B	ILE199
B	LEU201
B	TYR221
B	ASN222
B	LYS256
B	H4M402
B	HOH557
B	HOH564
B	HOH590
B	HOH591
B	HOH594
B	HOH602
B	HOH606
B	HOH613
B	HOH619
B	HOH621
B	HOH634
B	HOH645
B	HOH663

site_id	AC6
Number of Residues	18
Details	binding site for residue H4M B 402

Chain	Residue
B	ASN97
B	GLY98
B	THR235
B	LEU250
B	GLY253
B	GLY254
B	LYS256
B	NAP401
B	HOH516
B	HOH573
B	HOH593
B	HOH617
B	HOH621
B	HOH661
B	HOH694
B	SER16
B	PHE18
B	ASP19

site_id	AC7
Number of Residues	30
Details	binding site for residue NAP C 401

Chain	Residue
C	ASN97
C	THR102
C	ALA127
C	THR129
C	GLY130
C	PRO131
C	VAL132
C	GLY151
C	ARG152
C	LYS156
C	ALA196
C	GLY197
C	ALA198
C	ILE199
C	LEU201
C	TYR221
C	ASN222
C	LYS256
C	GOL402
C	HOH505
C	HOH529
C	HOH540
C	HOH563
C	HOH579
C	HOH594
C	HOH604
C	HOH613
C	HOH623
C	HOH624
C	HOH651

site_id	AC8
Number of Residues	8
Details	binding site for residue GOL C 402

Chain	Residue
C	PHE18
C	ASP19
C	ASN97
C	GLY98
C	LYS256
C	NAP401
C	HOH566
C	HOH641

site_id	AC9
Number of Residues	4
Details	binding site for residue GOL C 403

Chain	Residue
A	H4M404
A	HOH621
C	TYR51
C	PHE88

site_id	AD1
Number of Residues	2
Details	binding site for residue FMT C 404

Chain	Residue
C	GLY68
C	HOH510

site_id	AD2
Number of Residues	4
Details	binding site for residue FMT C 405

Chain	Residue
C	VAL111
C	LYS112
C	GLY116
C	LYS285

site_id	AD3
Number of Residues	32
Details	binding site for residue NAP D 401

Chain	Residue
D	ASN97
D	ALA127
D	THR129
D	GLY130
D	PRO131
D	VAL132
D	GLY151
D	ARG152
D	LYS156
D	ALA196
D	GLY197
D	ALA198
D	ILE199
D	LEU201
D	TYR221
D	ASN222
D	LYS256
D	HOH509
D	HOH510
D	HOH537
D	HOH556
D	HOH557
D	HOH578
D	HOH580
D	HOH584
D	HOH587
D	HOH595
D	HOH631
D	HOH645
D	HOH658
D	HOH688
F	HOH567

site_id	AD4
Number of Residues	3
Details	binding site for residue FMT D 402

Chain	Residue
D	ALA113
D	ALA114
D	GLU216

site_id	AD5
Number of Residues	6
Details	binding site for residue CL D 403

Chain	Residue
D	HIS30
D	HOH526
E	TYR24
E	HIS30
F	HIS30
F	HOH688

site_id	AD6
Number of Residues	30
Details	binding site for residue NAP E 401

Chain	Residue
E	ASN97
E	THR102
E	ALA127
E	THR129
E	GLY130
E	PRO131
E	VAL132
E	GLY151
E	ARG152
E	LYS156
E	ALA196
E	GLY197
E	ALA198
E	ILE199
E	LEU201
E	TYR221
E	ASN222
E	LYS256
E	HOH503
E	HOH506
E	HOH512
E	HOH537
E	HOH561
E	HOH581
E	HOH584
E	HOH597
E	HOH632
E	HOH649
E	HOH662
E	HOH666

site_id	AD7
Number of Residues	9
Details	binding site for residue GOL E 402

Chain	Residue
E	SER16
E	PHE18
E	ASP19
E	ASN97
E	GLY98
E	LYS256
E	HOH508
E	HOH547
E	HOH682

site_id	AD8
Number of Residues	5
Details	binding site for residue FMT E 403

Chain	Residue
B	LYS56
E	VAL37
E	HOH527
E	HOH575
E	HOH685

site_id	AD9
Number of Residues	7
Details	binding site for residue FMT E 404

Chain	Residue
D	GLU185
D	LYS188
E	TYR51
E	ARG53
E	GLY54
E	HOH524
E	HOH673

site_id	AE1
Number of Residues	5
Details	binding site for residue FMT E 405

Chain	Residue
E	SER2
E	ASP29
E	HOH522
E	HOH525
E	HOH556

site_id	AE2
Number of Residues	2
Details	binding site for residue FMT E 406

Chain	Residue
E	VAL274
E	HOH616

site_id	AE3
Number of Residues	3
Details	binding site for residue FMT E 407

Chain	Residue
E	PHE168
E	GLU278
E	HOH550

site_id	AE4
Number of Residues	34
Details	binding site for residue NAP F 401

Chain	Residue
F	ASN97
F	THR102
F	ALA127
F	THR129
F	GLY130
F	PRO131
F	VAL132
F	GLY151
F	ARG152
F	LYS156
F	ALA196
F	GLY197
F	ALA198
F	ILE199
F	LEU201
F	TYR221
F	ASN222
F	LYS256
F	GOL403
F	HOH518
F	HOH536
F	HOH539
F	HOH547
F	HOH548
F	HOH550
F	HOH557
F	HOH603
F	HOH613
F	HOH616
F	HOH633
F	HOH637
F	HOH652
F	HOH684
F	HOH700

site_id	AE5
Number of Residues	6
Details	binding site for residue MG F 402

Chain	Residue
D	ASP180
D	HOH503
D	HOH520
D	HOH586
D	HOH600
D	HOH730

site_id	AE6
Number of Residues	11
Details	binding site for residue GOL F 403

Chain	Residue
F	PHE18
F	ASP19
F	ASN97
F	GLY98
F	LYS256
F	NAP401
F	HOH501
F	HOH524
F	HOH535
F	HOH541
F	HOH582

site_id	AE7
Number of Residues	3
Details	binding site for residue GOL F 404

Chain	Residue
F	TYR51
F	HOH567
F	HOH617

site_id	AE8
Number of Residues	1
Details	binding site for residue GOL F 405

Chain	Residue
F	PHE85

site_id	AE9
Number of Residues	3
Details	binding site for residue FMT F 406

Chain	Residue
A	GLU146
F	ASN211
F	HOH505

site_id	AF1
Number of Residues	1
Details	binding site for residue FMT F 407

Chain	Residue
F	LYS237

site_id	AF2
Number of Residues	2
Details	binding site for residue FMT F 408

Chain	Residue
F	LYS166
F	ARG167

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	66
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11297742","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)