1YRQ
Structure of the ready oxidized form of [NiFe]-hydrogenase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| A | 0009055 | molecular_function | electron transfer activity |
| A | 0009061 | biological_process | anaerobic respiration |
| A | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| A | 0016020 | cellular_component | membrane |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0042597 | cellular_component | periplasmic space |
| A | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| A | 0051538 | molecular_function | 3 iron, 4 sulfur cluster binding |
| A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| B | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| B | 0009055 | molecular_function | electron transfer activity |
| B | 0009061 | biological_process | anaerobic respiration |
| B | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| B | 0016020 | cellular_component | membrane |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0042597 | cellular_component | periplasmic space |
| B | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| B | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0051538 | molecular_function | 3 iron, 4 sulfur cluster binding |
| B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| C | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| C | 0009055 | molecular_function | electron transfer activity |
| C | 0009061 | biological_process | anaerobic respiration |
| C | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| C | 0016020 | cellular_component | membrane |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0042597 | cellular_component | periplasmic space |
| C | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| C | 0051536 | molecular_function | iron-sulfur cluster binding |
| C | 0051538 | molecular_function | 3 iron, 4 sulfur cluster binding |
| C | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| D | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| D | 0009055 | molecular_function | electron transfer activity |
| D | 0009061 | biological_process | anaerobic respiration |
| D | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| D | 0016020 | cellular_component | membrane |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0042597 | cellular_component | periplasmic space |
| D | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| D | 0051536 | molecular_function | iron-sulfur cluster binding |
| D | 0051538 | molecular_function | 3 iron, 4 sulfur cluster binding |
| D | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| F | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| F | 0009055 | molecular_function | electron transfer activity |
| F | 0009061 | biological_process | anaerobic respiration |
| F | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| F | 0016020 | cellular_component | membrane |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0042597 | cellular_component | periplasmic space |
| F | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| F | 0051536 | molecular_function | iron-sulfur cluster binding |
| F | 0051538 | molecular_function | 3 iron, 4 sulfur cluster binding |
| F | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| G | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| G | 0009055 | molecular_function | electron transfer activity |
| G | 0009061 | biological_process | anaerobic respiration |
| G | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| G | 0016020 | cellular_component | membrane |
| G | 0016491 | molecular_function | oxidoreductase activity |
| G | 0042597 | cellular_component | periplasmic space |
| G | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
| G | 0046872 | molecular_function | metal ion binding |
| G | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| G | 0051536 | molecular_function | iron-sulfur cluster binding |
| G | 0051538 | molecular_function | 3 iron, 4 sulfur cluster binding |
| G | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
| H | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| H | 0016151 | molecular_function | nickel cation binding |
| H | 0016491 | molecular_function | oxidoreductase activity |
| H | 0042597 | cellular_component | periplasmic space |
| H | 0046872 | molecular_function | metal ion binding |
| H | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| I | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| I | 0016151 | molecular_function | nickel cation binding |
| I | 0016491 | molecular_function | oxidoreductase activity |
| I | 0042597 | cellular_component | periplasmic space |
| I | 0046872 | molecular_function | metal ion binding |
| I | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| J | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| J | 0016151 | molecular_function | nickel cation binding |
| J | 0016491 | molecular_function | oxidoreductase activity |
| J | 0042597 | cellular_component | periplasmic space |
| J | 0046872 | molecular_function | metal ion binding |
| J | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| K | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| K | 0016151 | molecular_function | nickel cation binding |
| K | 0016491 | molecular_function | oxidoreductase activity |
| K | 0042597 | cellular_component | periplasmic space |
| K | 0046872 | molecular_function | metal ion binding |
| K | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| M | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| M | 0016151 | molecular_function | nickel cation binding |
| M | 0016491 | molecular_function | oxidoreductase activity |
| M | 0042597 | cellular_component | periplasmic space |
| M | 0046872 | molecular_function | metal ion binding |
| M | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| N | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| N | 0016151 | molecular_function | nickel cation binding |
| N | 0016491 | molecular_function | oxidoreductase activity |
| N | 0042597 | cellular_component | periplasmic space |
| N | 0046872 | molecular_function | metal ion binding |
| N | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI H 551 |
| Chain | Residue |
| H | CYS72 |
| H | CYS75 |
| H | CYS543 |
| H | CYS546 |
| H | FCO550 |
| H | HOH557 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI I 551 |
| Chain | Residue |
| I | CYS546 |
| I | FCO550 |
| I | HOH557 |
| I | CYS72 |
| I | CYS75 |
| I | CYS543 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI J 551 |
| Chain | Residue |
| J | CYS72 |
| J | CYS75 |
| J | CYS543 |
| J | CYS546 |
| J | FCO550 |
| J | HOH557 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI K 551 |
| Chain | Residue |
| K | CYS72 |
| K | CYS75 |
| K | CYS543 |
| K | CYS546 |
| K | FCO550 |
| K | HOH557 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI M 551 |
| Chain | Residue |
| M | CYS72 |
| M | CYS75 |
| M | CYS543 |
| M | CYS546 |
| M | FCO550 |
| M | HOH557 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI N 551 |
| Chain | Residue |
| N | CYS72 |
| N | CYS75 |
| N | CYS543 |
| N | CYS546 |
| N | FCO550 |
| N | HOH557 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG H 553 |
| Chain | Residue |
| H | GLU53 |
| H | LEU495 |
| H | HIS549 |
| H | HOH554 |
| H | HOH555 |
| H | HOH556 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG I 553 |
| Chain | Residue |
| I | GLU53 |
| I | LEU495 |
| I | HIS549 |
| I | HOH554 |
| I | HOH555 |
| I | HOH556 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG J 553 |
| Chain | Residue |
| J | GLU53 |
| J | LEU495 |
| J | HIS549 |
| J | HOH554 |
| J | HOH555 |
| J | HOH556 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG K 553 |
| Chain | Residue |
| K | GLU53 |
| K | LEU495 |
| K | HIS549 |
| K | HOH554 |
| K | HOH555 |
| K | HOH556 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG M 553 |
| Chain | Residue |
| M | GLU53 |
| M | LEU495 |
| M | HIS549 |
| M | HOH554 |
| M | HOH555 |
| M | HOH556 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG N 553 |
| Chain | Residue |
| N | GLU53 |
| N | LEU495 |
| N | HIS549 |
| N | HOH554 |
| N | HOH555 |
| N | HOH556 |
| site_id | BC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SF4 A 265 |
| Chain | Residue |
| A | HIS184 |
| A | CYS187 |
| A | ARG189 |
| A | LEU190 |
| A | CYS212 |
| A | LEU213 |
| A | CYS218 |
| site_id | BC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S A 266 |
| Chain | Residue |
| A | ASN225 |
| A | CYS227 |
| A | PHE232 |
| A | CYS245 |
| A | LEU246 |
| A | GLY247 |
| A | CYS248 |
| H | LYS225 |
| H | GLN230 |
| site_id | BC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 A 267 |
| Chain | Residue |
| A | CYS17 |
| A | CYS20 |
| A | THR113 |
| A | CYS114 |
| A | GLY146 |
| A | CYS147 |
| A | PRO148 |
| H | ARG70 |
| site_id | BC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO H 550 |
| Chain | Residue |
| H | ALA474 |
| H | PRO475 |
| H | ARG476 |
| H | LEU479 |
| H | VAL497 |
| H | PRO498 |
| H | SER499 |
| H | CYS546 |
| H | NI551 |
| H | HOH557 |
| H | CYS75 |
| H | VAL78 |
| H | HIS79 |
| site_id | BC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SF4 B 265 |
| Chain | Residue |
| B | HIS184 |
| B | CYS187 |
| B | ARG189 |
| B | LEU190 |
| B | CYS212 |
| B | LEU213 |
| B | CYS218 |
| site_id | BC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S B 266 |
| Chain | Residue |
| B | ASN225 |
| B | CYS227 |
| B | PHE232 |
| B | TRP237 |
| B | CYS245 |
| B | LEU246 |
| B | CYS248 |
| I | LYS225 |
| I | GLN230 |
| site_id | CC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SF4 B 267 |
| Chain | Residue |
| B | GLU16 |
| B | CYS17 |
| B | CYS20 |
| B | GLY112 |
| B | THR113 |
| B | CYS114 |
| B | GLY146 |
| B | CYS147 |
| B | PRO148 |
| I | ARG70 |
| site_id | CC2 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO I 550 |
| Chain | Residue |
| I | CYS75 |
| I | VAL78 |
| I | HIS79 |
| I | ALA474 |
| I | PRO475 |
| I | ARG476 |
| I | LEU479 |
| I | VAL497 |
| I | PRO498 |
| I | SER499 |
| I | CYS546 |
| I | NI551 |
| I | HOH557 |
| site_id | CC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SF4 C 265 |
| Chain | Residue |
| C | HIS184 |
| C | CYS187 |
| C | ARG189 |
| C | LEU190 |
| C | CYS212 |
| C | LEU213 |
| C | CYS218 |
| site_id | CC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S C 266 |
| Chain | Residue |
| C | THR223 |
| C | ASN225 |
| C | CYS227 |
| C | PHE232 |
| C | TRP237 |
| C | CYS245 |
| C | LEU246 |
| C | CYS248 |
| J | GLN230 |
| site_id | CC5 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE SF4 C 267 |
| Chain | Residue |
| C | GLU16 |
| C | CYS17 |
| C | CYS20 |
| C | GLY112 |
| C | THR113 |
| C | CYS114 |
| C | GLY146 |
| C | CYS147 |
| C | PRO148 |
| J | ARG70 |
| J | HIS228 |
| site_id | CC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO J 550 |
| Chain | Residue |
| J | CYS75 |
| J | VAL78 |
| J | HIS79 |
| J | ALA474 |
| J | PRO475 |
| J | ARG476 |
| J | LEU479 |
| J | VAL497 |
| J | PRO498 |
| J | SER499 |
| J | CYS546 |
| J | NI551 |
| J | HOH557 |
| site_id | CC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 D 265 |
| Chain | Residue |
| D | HIS184 |
| D | CYS187 |
| D | ARG189 |
| D | LEU190 |
| D | CYS212 |
| D | LEU213 |
| D | CYS218 |
| D | PRO221 |
| site_id | CC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S D 266 |
| Chain | Residue |
| D | THR223 |
| D | ASN225 |
| D | CYS227 |
| D | PHE232 |
| D | CYS245 |
| D | LEU246 |
| D | CYS248 |
| K | LYS225 |
| K | GLN230 |
| site_id | CC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SF4 D 267 |
| Chain | Residue |
| D | GLU16 |
| D | CYS17 |
| D | CYS20 |
| D | THR113 |
| D | CYS114 |
| D | GLY146 |
| D | CYS147 |
| K | ARG70 |
| K | HIS228 |
| site_id | DC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE FCO K 550 |
| Chain | Residue |
| K | CYS75 |
| K | HIS79 |
| K | ALA474 |
| K | PRO475 |
| K | ARG476 |
| K | LEU479 |
| K | VAL497 |
| K | PRO498 |
| K | SER499 |
| K | CYS546 |
| K | NI551 |
| K | HOH557 |
| site_id | DC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 F 265 |
| Chain | Residue |
| F | HIS184 |
| F | CYS187 |
| F | ARG189 |
| F | LEU190 |
| F | CYS212 |
| F | LEU213 |
| F | CYS218 |
| F | PRO221 |
| site_id | DC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S F 266 |
| Chain | Residue |
| F | THR223 |
| F | ASN225 |
| F | CYS227 |
| F | PHE232 |
| F | TRP237 |
| F | CYS245 |
| F | LEU246 |
| F | CYS248 |
| M | GLN230 |
| site_id | DC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE SF4 F 267 |
| Chain | Residue |
| F | GLU16 |
| F | CYS17 |
| F | CYS20 |
| F | GLY112 |
| F | THR113 |
| F | CYS114 |
| F | GLY146 |
| F | CYS147 |
| F | PRO148 |
| M | ARG70 |
| M | HIS228 |
| site_id | DC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO M 550 |
| Chain | Residue |
| M | CYS75 |
| M | VAL78 |
| M | HIS79 |
| M | ALA474 |
| M | PRO475 |
| M | ARG476 |
| M | LEU479 |
| M | VAL497 |
| M | PRO498 |
| M | SER499 |
| M | CYS546 |
| M | NI551 |
| M | HOH557 |
| site_id | DC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SF4 G 265 |
| Chain | Residue |
| G | HIS184 |
| G | CYS187 |
| G | ARG189 |
| G | LEU190 |
| G | CYS212 |
| G | LEU213 |
| G | CYS218 |
| site_id | DC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S G 266 |
| Chain | Residue |
| G | ASN225 |
| G | CYS227 |
| G | PRO238 |
| G | CYS245 |
| G | LEU246 |
| G | CYS248 |
| G | HOH5277 |
| N | LYS225 |
| N | GLN230 |
| site_id | DC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SF4 G 267 |
| Chain | Residue |
| G | GLU16 |
| G | CYS17 |
| G | CYS20 |
| G | THR113 |
| G | CYS114 |
| G | CYS147 |
| G | PRO148 |
| N | ARG70 |
| N | HIS228 |
| site_id | DC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO N 550 |
| Chain | Residue |
| N | CYS75 |
| N | VAL78 |
| N | HIS79 |
| N | ALA474 |
| N | PRO475 |
| N | ARG476 |
| N | LEU479 |
| N | VAL497 |
| N | PRO498 |
| N | SER499 |
| N | CYS546 |
| N | NI551 |
| N | HOH557 |
Functional Information from PROSITE/UniProt
| site_id | PS00507 |
| Number of Residues | 26 |
| Details | NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGLEiilkgrdprdaqhftQRaCGVC |
| Chain | Residue | Details |
| H | ARG50-CYS75 |
| site_id | PS00508 |
| Number of Residues | 10 |
| Details | NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPCIACgv.H |
| Chain | Residue | Details |
| H | PHE540-HIS549 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 66 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| A | THR18 | |
| H | CYS543 | |
| H | GLU25 |
| site_id | CSA10 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| K | CYS543 |
| site_id | CSA11 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| M | CYS543 |
| site_id | CSA12 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| N | CYS543 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| I | CYS543 | |
| I | GLU25 | |
| B | THR18 |
| site_id | CSA3 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| J | CYS543 | |
| J | GLU25 | |
| C | THR18 |
| site_id | CSA4 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| D | THR18 | |
| K | CYS543 | |
| K | GLU25 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| F | THR18 | |
| M | CYS543 | |
| M | GLU25 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| N | CYS543 | |
| N | GLU25 | |
| G | THR18 |
| site_id | CSA7 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| H | CYS543 |
| site_id | CSA8 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| I | CYS543 |
| site_id | CSA9 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1cc1 |
| Chain | Residue | Details |
| J | CYS543 |
