3M32
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 | HOH716 |
| A | HOH1599 |
| site_id | AC3 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE TP7 A 553 |
| Chain | Residue |
| A | ARG270 |
| A | LEU320 |
| A | MET324 |
| A | SER325 |
| A | PHE330 |
| A | PHE443 |
| A | MET480 |
| A | ASN481 |
| A | VAL482 |
| A | HOH592 |
| A | HOH607 |
| A | HOH621 |
| A | HOH682 |
| A | HOH3684 |
| B | PHE362 |
| B | TYR367 |
| B | GLY368 |
| B | GLY369 |
| B | HIS379 |
| B | ILE380 |
| B | VAL381 |
| D | ARG225 |
| D | LYS256 |
| D | MHS257 |
| site_id | AC4 |
| Number of Residues | 40 |
| 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 | HOH582 |
| A | HOH651 |
| A | HOH673 |
| A | HOH675 |
| A | HOH697 |
| A | HOH699 |
| 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 | SHT555 |
| D | HOH667 |
| E | SER365 |
| E | ILE366 |
| E | TYR367 |
| F | LEU117 |
| F | SER118 |
| F | GLY119 |
| F | LYS153 |
| F | SER154 |
| F | VAL155 |
| F | HIS156 |
| F | HIS158 |
| site_id | AC5 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE COM A 554 |
| Chain | Residue |
| A | TYR333 |
| A | PHE443 |
| A | TYR444 |
| A | HOH3682 |
| A | HOH4145 |
| A | HOH4146 |
| B | PHE361 |
| B | TYR367 |
| C | LEU117 |
| C | ARG120 |
| D | F43552 |
| site_id | AC6 |
| Number of Residues | 26 |
| Details | BINDING SITE FOR RESIDUE SHT A 555 |
| Chain | Residue |
| A | HOH621 |
| A | HOH682 |
| A | HOH3684 |
| A | HOH4141 |
| A | HOH4145 |
| B | PHE362 |
| B | TYR367 |
| B | GLY368 |
| B | GLY369 |
| B | HIS379 |
| B | ILE380 |
| D | ARG225 |
| D | LYS256 |
| D | MHS257 |
| D | F43552 |
| A | ARG270 |
| A | LEU320 |
| A | MET324 |
| A | SER325 |
| A | PHE330 |
| A | TYR333 |
| A | PHE443 |
| A | MET480 |
| A | VAL482 |
| A | HOH592 |
| A | HOH607 |
| 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 | HOH641 |
| A | HOH1396 |
| A | HOH2285 |
| A | HOH3828 |
| A | HOH3971 |
| A | HOH3988 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO A 557 |
| Chain | Residue |
| A | TYR348 |
| site_id | AC9 |
| 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 | BC1 |
| 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 | BC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO B 445 |
| Chain | Residue |
| 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 | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 1 |
| Chain | Residue |
| B | ASP271 |
| B | HOH564 |
| B | HOH811 |
| B | HOH1206 |
| B | HOH3076 |
| B | HOH4161 |
| site_id | BC5 |
| 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 | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG C 1 |
| Chain | Residue |
| C | ARG43 |
| 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 | 40 |
| 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 | SHT555 |
| A | HOH600 |
| B | SER365 |
| B | ILE366 |
| B | TYR367 |
| C | LEU117 |
| C | SER118 |
| C | GLY119 |
| C | LYS153 |
| C | SER154 |
| C | VAL155 |
| C | HIS156 |
| C | HIS158 |
| D | ALA144 |
| D | VAL145 |
| D | VAL146 |
| D | GLN147 |
| D | GLN230 |
| D | MET233 |
| D | ALA243 |
| D | HOH569 |
| D | HOH647 |
| D | HOH648 |
| D | HOH671 |
| D | HOH711 |
| D | HOH720 |
| D | HOH722 |
| site_id | BC9 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE TP7 D 553 |
| 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 | HOH567 |
| D | HOH573 |
| D | HOH581 |
| D | HOH630 |
| D | HOH665 |
| D | HOH4142 |
| E | PHE362 |
| E | TYR367 |
| E | GLY368 |
| E | GLY369 |
| E | HIS379 |
| E | ILE380 |
| site_id | CC1 |
| Number of Residues | 11 |
| 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 |
| F | HOH4158 |
| site_id | CC2 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE SHT D 555 |
| Chain | Residue |
| A | F431 |
| A | ARG225 |
| A | LYS256 |
| A | MHS257 |
| D | ARG270 |
| D | LEU320 |
| D | MET324 |
| D | PHE330 |
| D | TYR333 |
| D | PHE443 |
| D | MET480 |
| D | VAL482 |
| D | HOH567 |
| D | HOH573 |
| D | HOH581 |
| D | HOH630 |
| D | HOH665 |
| D | HOH4142 |
| E | PHE362 |
| E | TYR367 |
| E | GLY368 |
| E | GLY369 |
| E | HIS379 |
| site_id | CC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO D 556 |
| Chain | Residue |
| D | TYR348 |
| site_id | CC4 |
| 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 | CC5 |
| 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 | CC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO F 251 |
| Chain | Residue |
| F | ARG43 |
| F | GLY46 |
| F | GLU47 |
| site_id | CC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO F 1 |
| Chain | Residue |
| F | GLN235 |
| F | ARG236 |
| F | VAL239 |
| F | HOH832 |
| F | HOH3289 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y |
| Chain | Residue | Details |
| C | ARG120 | |
| F | ARG120 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27140643, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:1MRO, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y, ECO:0007744|PDB:5G0R |
| Chain | Residue | Details |
| B | GLY369 | |
| E | GLY369 | |
| D | ARG225 | |
| D | LYS256 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: in chain B => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27140643, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:1MRO, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y, ECO:0007744|PDB:5G0R |
| Chain | Residue | Details |
| A | ARG270 | |
| D | ARG270 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957, ECO:0007744|PDB:1HBN, ECO:0007744|PDB:1MRO, ECO:0007744|PDB:3M1V, ECO:0007744|PDB:3POT, ECO:0007744|PDB:5A0Y |
| Chain | Residue | Details |
| A | TYR333 | |
| D | TYR333 | |
| D | TYR444 | |
| A | TYR444 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Pros-methylhistidine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
| Chain | Residue | Details |
| A | MHS257 | |
| D | MHS257 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: 5-methylarginine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
| Chain | Residue | Details |
| A | AGM271 | |
| D | AGM271 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: 2-methylglutamine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
| Chain | Residue | Details |
| A | MGN400 | |
| D | MGN400 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: 1-thioglycine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
| Chain | Residue | Details |
| A | GL3445 | |
| D | GL3445 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: (Z)-2,3-didehydroaspartate => ECO:0000269|PubMed:27467699 |
| Chain | Residue | Details |
| A | ASP450 | |
| D | ASP450 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: S-methylcysteine => ECO:0000269|PubMed:10660523, ECO:0000269|PubMed:11491299, ECO:0000269|PubMed:20707311, ECO:0000269|PubMed:21438550, ECO:0000269|PubMed:27467699, ECO:0000269|PubMed:9367957 |
| Chain | Residue | Details |
| A | SMC452 | |
| D | SMC452 |
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 | TYR333 | electrostatic stabiliser, radical stabiliser |
| A | GL3445 | single electron acceptor, single electron donor, single electron relay |
| A | ASN481 | 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 | TYR333 | electrostatic stabiliser, radical stabiliser |
| D | GL3445 | single electron acceptor, single electron donor, single electron relay |
| D | ASN481 | activator, electrostatic stabiliser, proton acceptor, proton donor, proton relay |
