3POT
Structural analysis of a Ni(III)-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis
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 | 3 |
| Details | BINDING SITE FOR RESIDUE MG A 551 |
| Chain | Residue |
| A | HOH850 |
| A | HOH3425 |
| D | HOH899 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 552 |
| Chain | Residue |
| A | HOH600 |
| A | HOH725 |
| A | HOH1212 |
| A | HOH1508 |
| A | HOH1856 |
| A | HOH2090 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 553 |
| Chain | Residue |
| A | HOH1159 |
| A | HOH1212 |
| A | HOH1456 |
| A | HOH1481 |
| A | HOH1508 |
| A | HOH1968 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 554 |
| Chain | Residue |
| A | HOH1037 |
| A | HOH1115 |
| A | HOH3449 |
| A | HOH3450 |
| site_id | AC5 |
| Number of Residues | 40 |
| Details | BINDING SITE FOR RESIDUE F43 A 555 |
| Chain | Residue |
| A | ALA144 |
| A | VAL145 |
| A | VAL146 |
| A | GLN147 |
| A | GLN230 |
| A | MET233 |
| A | ALA243 |
| A | HOH577 |
| A | HOH615 |
| A | HOH619 |
| A | HOH624 |
| A | HOH671 |
| A | HOH747 |
| 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 | COM555 |
| D | 06C556 |
| D | HOH626 |
| E | SER365 |
| E | ILE366 |
| E | TYR367 |
| F | LEU117 |
| F | SER118 |
| F | GLY119 |
| F | LYS153 |
| F | SER154 |
| F | VAL155 |
| F | HIS156 |
| F | HIS158 |
| F | HOH262 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE COM A 556 |
| Chain | Residue |
| A | TYR333 |
| A | PHE443 |
| A | TYR444 |
| A | HOH733 |
| B | PHE361 |
| B | TYR367 |
| C | LEU117 |
| C | ARG120 |
| D | F43552 |
| site_id | AC7 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE TXZ A 557 |
| Chain | Residue |
| A | ARG270 |
| A | MET324 |
| A | PHE330 |
| A | PHE443 |
| A | MET480 |
| A | ASN481 |
| A | VAL482 |
| A | HOH613 |
| A | HOH628 |
| A | HOH637 |
| A | HOH715 |
| A | HOH726 |
| B | GLY368 |
| B | GLY369 |
| B | HIS379 |
| B | ILE380 |
| D | ARG225 |
| D | LYS256 |
| D | MHS257 |
| site_id | AC8 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE TP7 A 558 |
| Chain | Residue |
| A | HOH715 |
| A | HOH726 |
| 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 | PHE443 |
| A | MET480 |
| A | ASN481 |
| A | VAL482 |
| A | HOH613 |
| A | HOH628 |
| A | HOH637 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE 06C A 559 |
| Chain | Residue |
| A | TYR333 |
| B | TYR367 |
| D | F43552 |
| site_id | BC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE K A 561 |
| Chain | Residue |
| A | ARG102 |
| A | SER215 |
| A | ARG216 |
| A | CYS218 |
| D | ARG102 |
| D | SER215 |
| D | ARG216 |
| D | CYS218 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 444 |
| Chain | Residue |
| B | HOH1103 |
| B | HOH1305 |
| B | HOH2344 |
| B | HOH3452 |
| B | HOH3453 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 445 |
| Chain | Residue |
| B | ASP271 |
| B | HOH670 |
| B | HOH976 |
| B | HOH1040 |
| B | HOH1911 |
| B | HOH2168 |
| site_id | BC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 250 |
| Chain | Residue |
| C | GLU30 |
| C | HOH726 |
| C | HOH3417 |
| C | HOH3418 |
| C | HOH3419 |
| C | HOH3420 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MG C 251 |
| Chain | Residue |
| A | HOH3614 |
| C | HOH1328 |
| C | HOH1849 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 551 |
| Chain | Residue |
| D | HOH1211 |
| D | HOH1613 |
| D | HOH3428 |
| D | HOH3429 |
| D | HOH3430 |
| E | HOH1573 |
| site_id | BC7 |
| Number of Residues | 41 |
| 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 | COM556 |
| A | 06C559 |
| A | HOH609 |
| B | SER365 |
| B | ILE366 |
| B | TYR367 |
| C | LEU117 |
| C | SER118 |
| C | GLY119 |
| C | ARG120 |
| C | LYS153 |
| C | SER154 |
| C | VAL155 |
| C | HIS156 |
| C | HIS158 |
| C | HOH264 |
| D | ALA144 |
| D | VAL145 |
| D | VAL146 |
| D | GLN147 |
| D | GLN230 |
| D | MET233 |
| D | ALA243 |
| D | HOH582 |
| D | HOH610 |
| D | HOH619 |
| D | HOH640 |
| D | HOH649 |
| D | HOH700 |
| site_id | BC8 |
| 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 | HOH568 |
| D | HOH580 |
| D | HOH606 |
| D | HOH607 |
| D | HOH716 |
| E | PHE362 |
| E | TYR367 |
| E | GLY368 |
| E | GLY369 |
| E | HIS379 |
| E | ILE380 |
| site_id | BC9 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE TXZ D 554 |
| Chain | Residue |
| A | ARG225 |
| A | LYS256 |
| A | MHS257 |
| D | ARG270 |
| D | MET324 |
| D | PHE330 |
| D | PHE443 |
| D | MET480 |
| D | ASN481 |
| D | VAL482 |
| D | HOH568 |
| D | HOH580 |
| D | HOH606 |
| D | HOH607 |
| D | HOH716 |
| E | PHE362 |
| E | GLY369 |
| E | HIS379 |
| E | ILE380 |
| site_id | CC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE COM D 555 |
| Chain | Residue |
| A | F43555 |
| D | TYR333 |
| D | PHE443 |
| D | TYR444 |
| D | HOH713 |
| E | PHE361 |
| E | SER365 |
| E | TYR367 |
| F | LEU117 |
| F | ARG120 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE 06C D 556 |
| Chain | Residue |
| A | F43555 |
| D | TYR333 |
| E | TYR367 |
| site_id | CC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO D 558 |
| Chain | Residue |
| D | TYR348 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG E 444 |
| Chain | Residue |
| E | HOH1993 |
| E | HOH2253 |
| E | HOH3439 |
| E | HOH3440 |
| site_id | CC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG E 445 |
| Chain | Residue |
| C | HOH3555 |
| E | ASP147 |
| E | HOH1070 |
| E | HOH1373 |
| E | HOH3557 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG F 250 |
| Chain | Residue |
| F | GLU30 |
| F | HOH635 |
| F | HOH648 |
| F | HOH3422 |
| F | HOH3423 |
| F | HOH3424 |
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 | |
| A | TYR444 | |
| D | TYR333 | |
| D | 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 |
