Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3M30

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	HOH1356
A	HOH1590
A	HOH1599
A	HOH2583
A	HOH2603
A	HOH3581

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG A 552

Chain	Residue
A	HOH2285
A	HOH3581
A	HOH3828
A	HOH3971
A	ACT556
A	HOH713
A	HOH1599

site_id	AC3
Number of Residues	39
Details	BINDING SITE FOR RESIDUE F43 A 1

Chain	Residue
A	ALA144
A	VAL145
A	VAL146
A	GLN147
A	GLN230
A	MET233
A	ALA243
A	HOH651
A	HOH673
A	HOH675
A	HOH695
A	HOH697
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	COM554
D	HOH664
E	SER365
E	ILE366
E	TYR367
F	LEU117
F	SER118
F	GLY119
F	LYS153
F	SER154
F	VAL155
F	HIS156
F	HIS158
F	HOH582

site_id	AC4
Number of Residues	22
Details	BINDING SITE FOR RESIDUE TP7 A 553

Chain	Residue
A	ARG270
A	LEU320
A	MET324
A	PHE330
A	PHE443
A	MET480
A	ASN481
A	VAL482
A	HOH592
A	HOH607
A	HOH622
A	HOH682
A	HOH3684
B	PHE362
B	TYR367
B	GLY368
B	GLY369
B	HIS379
B	ILE380
D	ARG225
D	LYS256
D	MHS257

site_id	AC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE COM A 554

Chain	Residue
A	TYR333
A	PHE443
A	TYR444
A	XP9555
A	HOH3682
B	PHE361
B	SER365
B	TYR367
C	LEU117
C	ARG120
D	F43552

site_id	AC6
Number of Residues	26
Details	BINDING SITE FOR RESIDUE XP9 A 555

Chain	Residue
A	HOH682
A	HOH3684
B	PHE361
B	PHE362
B	TYR367
B	GLY368
B	GLY369
B	HIS379
B	ILE380
D	ARG225
D	LYS256
D	MHS257
A	ARG270
A	LEU320
A	MET324
A	SER325
A	PHE330
A	TYR333
A	PHE443
A	MET480
A	ASN481
A	VAL482
A	COM554
A	HOH592
A	HOH607
A	HOH622

site_id	AC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ACT A 556

Chain	Residue
A	VAL519
A	LYS531
A	PHE537
A	GLU538
A	MG552
A	HOH642
A	HOH1396
A	HOH2285
A	HOH3828
A	HOH3971
A	HOH3988

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ZN A 558

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

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 444

Chain	Residue
B	HOH1305
B	HOH3547
B	HOH3548
B	HOH3549
B	HOH3550
B	HOH3714

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 445

Chain	Residue
B	ASP271
B	HOH564
B	HOH811
B	HOH1206
B	HOH3076
B	HOH4102

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO B 446

Chain	Residue
B	LYS257
B	LYS261

site_id	BC3
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	BC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ACT C 1

Chain	Residue
C	PRO50
C	SER51
C	VAL52
C	ARG81
D	LYS118
D	ARG119
D	GLY121

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 251

Chain	Residue
C	ARG236
C	HOH856
C	HOH3762

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG C 252

Chain	Residue
C	GLY46
C	GLU47
C	GLU48
C	TYR49
C	HOH3630

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 1

Chain	Residue
D	HOH3543
D	HOH3544
D	HOH3546
F	HOH3542
F	HOH3545

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 551

Chain	Residue
D	HOH1116
D	HOH3559
D	HOH3560
D	HOH3561
D	HOH3562
D	HOH3563

site_id	BC9
Number of Residues	39
Details	BINDING SITE FOR RESIDUE F43 D 552

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	COM554
A	HOH600
B	SER365
B	ILE366
B	TYR367
C	LEU117
C	SER118
C	GLY119
C	LYS153
C	SER154
C	VAL155
C	HIS156
C	HIS158
C	HOH647
D	ALA144
D	VAL145
D	VAL146
D	GLN147
D	GLN230
D	MET233
D	ALA243
D	HOH567
D	HOH643
D	HOH668
D	HOH707
D	HOH717
D	HOH719

site_id	CC1
Number of Residues	22
Details	BINDING SITE FOR RESIDUE TP7 D 553

Chain	Residue
A	ARG225
A	LYS256
A	MHS257
D	ARG270
D	LEU320
D	MET324
D	PHE330
D	PHE443
D	MET480
D	ASN481
D	VAL482
D	HOH566
D	HOH571
D	HOH579
D	HOH628
D	HOH662
E	PHE362
E	TYR367
E	GLY368
E	GLY369
E	HIS379
E	ILE380

site_id	CC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE COM D 554

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

site_id	CC3
Number of Residues	25
Details	BINDING SITE FOR RESIDUE XP9 D 555

Chain	Residue
A	ARG225
A	LYS256
A	MHS257
D	ARG270
D	LEU320
D	MET324
D	SER325
D	PHE330
D	TYR333
D	PHE443
D	MET480
D	ASN481
D	VAL482
D	HOH566
D	HOH571
D	HOH579
D	HOH628
D	HOH662
E	PHE361
E	PHE362
E	TYR367
E	GLY368
E	GLY369
E	HIS379
E	ILE380

site_id	CC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO D 556

Chain	Residue
D	TYR348

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 444

Chain	Residue
E	HOH2200
E	HOH2328
E	HOH3583
E	HOH3584
E	HOH3585

site_id	CC6
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

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO F 251

Chain	Residue
F	GLN235
F	ARG236
F	VAL239
F	HOH832
F	HOH3289

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO F 252

Chain	Residue
F	LYS132
F	GLU136
F	HOH1243

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)