Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3M2V

Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0015948	biological_process	methanogenesis
A	0016740	molecular_function	transferase activity
A	0046872	molecular_function	metal ion binding
A	0050524	molecular_function	coenzyme-B sulfoethylthiotransferase activity
B	0005737	cellular_component	cytoplasm
B	0015948	biological_process	methanogenesis
B	0016740	molecular_function	transferase activity
B	0050524	molecular_function	coenzyme-B sulfoethylthiotransferase activity
C	0005737	cellular_component	cytoplasm
C	0015948	biological_process	methanogenesis
C	0016740	molecular_function	transferase activity
C	0050524	molecular_function	coenzyme-B sulfoethylthiotransferase activity
D	0005737	cellular_component	cytoplasm
D	0015948	biological_process	methanogenesis
D	0016740	molecular_function	transferase activity
D	0046872	molecular_function	metal ion binding
D	0050524	molecular_function	coenzyme-B sulfoethylthiotransferase activity
E	0005737	cellular_component	cytoplasm
E	0015948	biological_process	methanogenesis
E	0016740	molecular_function	transferase activity
E	0050524	molecular_function	coenzyme-B sulfoethylthiotransferase activity
F	0005737	cellular_component	cytoplasm
F	0015948	biological_process	methanogenesis
F	0016740	molecular_function	transferase activity
F	0050524	molecular_function	coenzyme-B sulfoethylthiotransferase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 551

Chain	Residue
A	ACT555
A	HOH706
A	HOH1599
A	HOH2285
A	HOH3828
A	HOH3971

site_id	AC2
Number of Residues	39
Details	BINDING SITE FOR RESIDUE F43 A 1

Chain	Residue
A	GLN147
A	GLN230
A	MET233
A	ALA243
A	HOH647
A	HOH666
A	HOH668
A	HOH671
A	HOH690
A	HOH692
A	HOH788
D	GLY326
D	GLY327
D	VAL328
D	GLY329
D	PHE330
D	THR331
D	GLN332
D	TYR333
D	PHE396
D	GLY397
D	GLY442
D	PHE443
D	COM552
E	SER365
E	ILE366
E	TYR367
F	LEU117
F	SER118
F	GLY119
F	LYS153
F	SER154
F	VAL155
F	HIS156
F	HIS158
F	HOH582
A	ALA144
A	VAL145
A	VAL146

site_id	AC3
Number of Residues	21
Details	BINDING SITE FOR RESIDUE TP7 A 552

Chain	Residue
A	ARG270
A	LEU320
A	MET324
A	PHE330
A	PHE443
A	MET480
A	ASN481
A	VAL482
A	HOH588
A	HOH600
A	HOH678
A	HOH3684
B	PHE362
B	TYR367
B	GLY369
B	HIS379
B	ILE380
B	HOH479
D	ARG225
D	LYS256
D	MHS257

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE COM A 553

Chain	Residue
A	TYR333
A	PHE443
A	TYR444
A	HOH3682
B	PHE361
B	SER365
B	TYR367
C	LEU117
C	ARG120
D	F43551

site_id	AC5
Number of Residues	20
Details	BINDING SITE FOR RESIDUE XP8 A 554

Chain	Residue
A	ARG270
A	LEU320
A	MET324
A	PHE330
A	PHE443
A	MET480
A	HOH588
A	HOH600
A	HOH678
A	HOH3684
B	PHE361
B	PHE362
B	TYR367
B	GLY369
B	HIS379
B	ILE380
B	HOH479
D	ARG225
D	LYS256
D	MHS257

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ACT A 555

Chain	Residue
A	GLU538
A	MG551
A	HOH1396
A	HOH2285
A	HOH3828
A	HOH3988
A	HOH4121
A	VAL519
A	LYS531
A	PHE537

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 556

Chain	Residue
A	ASP516
A	LEU518
A	PHE520
A	ASP521
A	HOH1599
A	HOH2603

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 557

Chain	Residue
A	TYR348
A	HOH4125

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 1

Chain	Residue
B	HOH1305
B	HOH3547
B	HOH3548
B	HOH3549
B	HOH3550

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 444

Chain	Residue
B	ASP271
B	HOH811
B	HOH1206
B	HOH3076
B	HOH4122

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 250

Chain	Residue
C	GLU30
C	HOH1095
C	HOH3555
C	HOH3556
C	HOH3557
C	HOH3558

site_id	BC3
Number of Residues	38
Details	BINDING SITE FOR RESIDUE F43 D 551

Chain	Residue
A	GLY326
A	GLY327
A	VAL328
A	GLY329
A	PHE330
A	THR331
A	GLN332
A	TYR333
A	PHE396
A	GLY397
A	GLY442
A	PHE443
A	COM553
B	SER365
B	ILE366
B	TYR367
C	LEU117
C	SER118
C	GLY119
C	LYS153
C	SER154
C	VAL155
C	HIS156
C	HIS158
C	HOH526
D	ALA144
D	VAL145
D	VAL146
D	GLN147
D	GLN230
D	MET233
D	ALA243
D	HOH567
D	HOH594
D	HOH641
D	HOH665
D	HOH707
D	HOH716

site_id	BC4
Number of Residues	22
Details	BINDING SITE FOR RESIDUE TP7 D 1

Chain	Residue
A	ARG225
A	LYS256
A	MHS257
D	ARG270
D	LEU320
D	MET324
D	SER325
D	PHE330
D	PHE443
D	MET480
D	ASN481
D	VAL482
D	HOH566
D	HOH571
D	HOH579
D	HOH627
D	HOH660
E	PHE362
E	TYR367
E	GLY369
E	HIS379
E	ILE380

site_id	BC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE COM D 552

Chain	Residue
A	F431
D	TYR333
D	PHE443
D	TYR444
E	PHE361
E	SER365
E	TYR367
F	LEU117
F	ARG120
F	HOH760

site_id	BC6
Number of Residues	19
Details	BINDING SITE FOR RESIDUE XP8 D 553

Chain	Residue
A	ARG225
A	LYS256
A	MHS257
D	ARG270
D	LEU320
D	MET324
D	PHE330
D	PHE443
D	MET480
D	HOH566
D	HOH571
D	HOH579
D	HOH627
D	HOH660
E	PHE362
E	TYR367
E	GLY369
E	HIS379
E	ILE380

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 554

Chain	Residue
D	LYS22
F	GLU164
F	GLY166

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO D 555

Chain	Residue
D	TYR348

site_id	BC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ZN D 556

Chain	Residue
A	ARG102
A	SER215
A	ARG216
A	CYS218
D	ARG102
D	SER215
D	ARG216
D	CYS218

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 250

Chain	Residue
F	GLU30
F	HOH1294
F	HOH3551
F	HOH3552
F	HOH3553
F	HOH3554

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Binding site: {"description":"axial binding residue","evidences":[{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27140643","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1HBN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MRO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3M1V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3POT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A0Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5G0R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Binding site: {"description":"in chain A","evidences":[{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27140643","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1HBN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MRO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3M1V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3POT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A0Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5G0R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Binding site: {"description":"in chain B","evidences":[{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27140643","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1HBN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MRO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3M1V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3POT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A0Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5G0R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1HBN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MRO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3M1V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3POT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A0Y","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"Pros-methylhistidine","evidences":[{"source":"PubMed","id":"10660523","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"5-methylarginine","evidences":[{"source":"PubMed","id":"10660523","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"2-methylglutamine","evidences":[{"source":"PubMed","id":"10660523","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"1-thioglycine","evidences":[{"source":"PubMed","id":"10660523","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"(Z)-2,3-didehydroaspartate","evidences":[{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"S-methylcysteine","evidences":[{"source":"PubMed","id":"10660523","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27140643","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9367957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1HBN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MRO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3M1V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3POT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A0Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5G0R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11491299","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20707311","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21438550","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27467699","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1HBN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3M1V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3POT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A0Y","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	1
Details	M-CSA 156

Chain	Residue	Details
B	TYR367	electrostatic stabiliser, proton acceptor, proton donor, proton relay, radical stabiliser
A	ASN341	electrostatic stabiliser, radical stabiliser
A	VAL457	single electron acceptor, single electron donor, single electron relay
A	ASP501	activator, electrostatic stabiliser, proton acceptor, proton donor, proton relay

site_id	MCSA2
Number of Residues	1
Details	M-CSA 156

Chain	Residue	Details
E	TYR367	electrostatic stabiliser, proton acceptor, proton donor, proton relay, radical stabiliser
D	ASN341	electrostatic stabiliser, radical stabiliser
D	VAL457	single electron acceptor, single electron donor, single electron relay
D	ASP501	activator, electrostatic stabiliser, proton acceptor, proton donor, proton relay

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