6Z7R
Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Krypton gas - structure wtKr1
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| A | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| B | 0016151 | molecular_function | nickel cation binding |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0042597 | cellular_component | periplasmic space |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| C | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| C | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| C | 0051536 | molecular_function | iron-sulfur cluster binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| D | 0016151 | molecular_function | nickel cation binding |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0042597 | cellular_component | periplasmic space |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 A 301 |
| Chain | Residue |
| A | HIS208 |
| A | CYS211 |
| A | TYR217 |
| A | CYS232 |
| A | ARG233 |
| A | CYS238 |
| A | GLY240 |
| A | VAL260 |
| site_id | AC2 |
| Number of Residues | 9 |
| Details | binding site for residue SF4 A 302 |
| Chain | Residue |
| A | CYS247 |
| A | TRP252 |
| A | CYS259 |
| A | CYS265 |
| A | ILE266 |
| A | GLY267 |
| A | CYS268 |
| B | ARG182 |
| A | THR243 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | binding site for residue SF4 A 303 |
| Chain | Residue |
| A | GLY17 |
| A | CYS18 |
| A | CYS21 |
| A | GLY119 |
| A | THR120 |
| A | CYS121 |
| A | GLY158 |
| A | CYS159 |
| A | 6ML304 |
| B | ARG73 |
| B | HIS185 |
| site_id | AC4 |
| Number of Residues | 16 |
| Details | binding site for residue 6ML A 304 |
| Chain | Residue |
| A | CYS18 |
| A | THR19 |
| A | GLY20 |
| A | CYS21 |
| A | GLU77 |
| A | GLY78 |
| A | GLY119 |
| A | THR120 |
| A | CYS121 |
| A | GLY158 |
| A | CYS159 |
| A | PRO160 |
| A | SF4303 |
| A | HOH413 |
| B | ARG73 |
| B | HIS185 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue KR A 306 |
| Chain | Residue |
| A | VAL10 |
| A | VAL170 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue KR A 307 |
| Chain | Residue |
| A | PHE73 |
| A | LEU174 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | binding site for residue KR A 308 |
| Chain | Residue |
| A | VAL36 |
| A | KR309 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | binding site for residue KR A 309 |
| Chain | Residue |
| A | KR308 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue KR A 311 |
| Chain | Residue |
| A | LEU116 |
| A | ALA173 |
| site_id | AD1 |
| Number of Residues | 1 |
| Details | binding site for residue KR A 312 |
| Chain | Residue |
| A | LEU26 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue KR A 313 |
| Chain | Residue |
| A | PRO152 |
| A | VAL154 |
| A | VAL189 |
| site_id | AD3 |
| Number of Residues | 2 |
| Details | binding site for residue KR A 314 |
| Chain | Residue |
| A | ILE58 |
| A | ILE91 |
| site_id | AD4 |
| Number of Residues | 1 |
| Details | binding site for residue KR A 315 |
| Chain | Residue |
| A | LEU172 |
| site_id | AD5 |
| Number of Residues | 12 |
| Details | binding site for residue FCO B 501 |
| Chain | Residue |
| B | CYS78 |
| B | HIS82 |
| B | ALA420 |
| B | PRO421 |
| B | ARG422 |
| B | LEU425 |
| B | ALA444 |
| B | SER445 |
| B | SEC489 |
| B | CYS492 |
| B | NI502 |
| B | H2S504 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue NI B 502 |
| Chain | Residue |
| B | CSD75 |
| B | CYS78 |
| B | SEC489 |
| B | CYS492 |
| B | FCO501 |
| B | H2S504 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue FE2 B 503 |
| Chain | Residue |
| B | GLU56 |
| B | ILE441 |
| B | HIS495 |
| B | HOH602 |
| B | HOH610 |
| B | HOH611 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue CL B 505 |
| Chain | Residue |
| B | CYS78 |
| B | THR80 |
| B | ALA81 |
| B | PHE110 |
| B | ASN113 |
| B | PRO421 |
| site_id | AD9 |
| Number of Residues | 3 |
| Details | binding site for residue KR B 506 |
| Chain | Residue |
| B | TYR123 |
| B | GLY158 |
| B | KR507 |
| site_id | AE1 |
| Number of Residues | 3 |
| Details | binding site for residue KR B 507 |
| Chain | Residue |
| B | PHE122 |
| B | ILE228 |
| B | KR506 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue KR B 508 |
| Chain | Residue |
| B | KR509 |
| B | GLN128 |
| B | VAL131 |
| B | TYR162 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue KR B 509 |
| Chain | Residue |
| B | PRO134 |
| B | PHE139 |
| B | TYR162 |
| B | KR508 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue KR B 510 |
| Chain | Residue |
| B | LEU150 |
| B | LEU154 |
| B | GLY158 |
| B | VAL224 |
| B | ILE228 |
| site_id | AE5 |
| Number of Residues | 1 |
| Details | binding site for residue KR B 511 |
| Chain | Residue |
| B | TYR162 |
| site_id | AE6 |
| Number of Residues | 1 |
| Details | binding site for residue KR B 512 |
| Chain | Residue |
| B | PHE353 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue KR B 513 |
| Chain | Residue |
| B | ASN337 |
| B | PRO339 |
| B | TYR384 |
| site_id | AE8 |
| Number of Residues | 9 |
| Details | binding site for residue SF4 C 301 |
| Chain | Residue |
| C | HIS208 |
| C | CYS211 |
| C | TYR213 |
| C | LEU214 |
| C | CYS232 |
| C | ARG233 |
| C | TYR234 |
| C | CYS238 |
| C | VAL260 |
| site_id | AE9 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 C 302 |
| Chain | Residue |
| C | THR243 |
| C | CYS247 |
| C | TRP252 |
| C | CYS259 |
| C | CYS265 |
| C | ILE266 |
| C | CYS268 |
| D | ARG182 |
| site_id | AF1 |
| Number of Residues | 11 |
| Details | binding site for residue SF4 C 303 |
| Chain | Residue |
| C | GLY17 |
| C | CYS18 |
| C | CYS21 |
| C | GLY119 |
| C | THR120 |
| C | CYS121 |
| C | GLY158 |
| C | CYS159 |
| C | 6ML304 |
| D | ARG73 |
| D | HIS185 |
| site_id | AF2 |
| Number of Residues | 16 |
| Details | binding site for residue 6ML C 304 |
| Chain | Residue |
| C | CYS18 |
| C | THR19 |
| C | GLY20 |
| C | CYS21 |
| C | GLU77 |
| C | GLY78 |
| C | GLY119 |
| C | THR120 |
| C | CYS121 |
| C | GLY158 |
| C | CYS159 |
| C | PRO160 |
| C | SF4303 |
| C | HOH404 |
| D | ARG73 |
| D | HIS185 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue KR C 306 |
| Chain | Residue |
| C | VAL10 |
| C | LEU116 |
| C | VAL170 |
| C | KR311 |
| site_id | AF4 |
| Number of Residues | 2 |
| Details | binding site for residue KR C 307 |
| Chain | Residue |
| C | PHE73 |
| C | LEU174 |
| site_id | AF5 |
| Number of Residues | 1 |
| Details | binding site for residue KR C 308 |
| Chain | Residue |
| C | ALA173 |
| site_id | AF6 |
| Number of Residues | 1 |
| Details | binding site for residue KR C 309 |
| Chain | Residue |
| C | LEU26 |
| site_id | AF7 |
| Number of Residues | 1 |
| Details | binding site for residue KR C 310 |
| Chain | Residue |
| C | KR311 |
| site_id | AF8 |
| Number of Residues | 3 |
| Details | binding site for residue KR C 311 |
| Chain | Residue |
| C | KR306 |
| C | KR310 |
| C | KR312 |
| site_id | AF9 |
| Number of Residues | 4 |
| Details | binding site for residue KR C 312 |
| Chain | Residue |
| C | VAL75 |
| C | LEU116 |
| C | ILE166 |
| C | KR311 |
| site_id | AG1 |
| Number of Residues | 2 |
| Details | binding site for residue KR C 314 |
| Chain | Residue |
| C | PRO152 |
| C | VAL154 |
| site_id | AG2 |
| Number of Residues | 2 |
| Details | binding site for residue KR C 315 |
| Chain | Residue |
| C | LEU172 |
| C | VAL192 |
| site_id | AG3 |
| Number of Residues | 2 |
| Details | binding site for residue KR C 316 |
| Chain | Residue |
| C | ILE58 |
| C | MET61 |
| site_id | AG4 |
| Number of Residues | 5 |
| Details | binding site for residue KR C 317 |
| Chain | Residue |
| C | ILE127 |
| C | PHE273 |
| D | GLN69 |
| D | ILE70 |
| D | ARG73 |
| site_id | AG5 |
| Number of Residues | 11 |
| Details | binding site for residue FCO D 501 |
| Chain | Residue |
| D | CYS78 |
| D | ALA420 |
| D | PRO421 |
| D | ARG422 |
| D | LEU425 |
| D | ALA444 |
| D | SER445 |
| D | SEC489 |
| D | CYS492 |
| D | NI502 |
| D | H2S504 |
| site_id | AG6 |
| Number of Residues | 6 |
| Details | binding site for residue NI D 502 |
| Chain | Residue |
| D | CSD75 |
| D | CYS78 |
| D | SEC489 |
| D | CYS492 |
| D | FCO501 |
| D | H2S504 |
| site_id | AG7 |
| Number of Residues | 5 |
| Details | binding site for residue FE2 D 503 |
| Chain | Residue |
| D | GLU56 |
| D | ILE441 |
| D | HIS495 |
| D | HOH603 |
| D | HOH604 |
| site_id | AG8 |
| Number of Residues | 6 |
| Details | binding site for residue CL D 505 |
| Chain | Residue |
| D | CYS78 |
| D | THR80 |
| D | ALA81 |
| D | PHE110 |
| D | ASN113 |
| D | PRO421 |
| site_id | AG9 |
| Number of Residues | 5 |
| Details | binding site for residue KR D 506 |
| Chain | Residue |
| D | PHE122 |
| D | TYR123 |
| D | ALA127 |
| D | GLY158 |
| D | ILE228 |
| site_id | AH1 |
| Number of Residues | 2 |
| Details | binding site for residue KR D 507 |
| Chain | Residue |
| D | TYR162 |
| D | KR510 |
| site_id | AH2 |
| Number of Residues | 3 |
| Details | binding site for residue KR D 508 |
| Chain | Residue |
| D | LEU426 |
| D | VAL442 |
| D | TRP447 |
| site_id | AH3 |
| Number of Residues | 1 |
| Details | binding site for residue KR D 509 |
| Chain | Residue |
| D | TYR162 |
| site_id | AH4 |
| Number of Residues | 4 |
| Details | binding site for residue KR D 510 |
| Chain | Residue |
| D | PRO134 |
| D | PHE139 |
| D | TYR162 |
| D | KR507 |
| site_id | AH5 |
| Number of Residues | 5 |
| Details | binding site for residue KR D 511 |
| Chain | Residue |
| D | LEU150 |
| D | LEU154 |
| D | GLY158 |
| D | VAL224 |
| D | ILE228 |
| site_id | AH6 |
| Number of Residues | 1 |
| Details | binding site for residue KR D 512 |
| Chain | Residue |
| D | PHE236 |
| site_id | AH7 |
| Number of Residues | 13 |
| Details | binding site for residues H2S B 504 and SEC B 489 |
| Chain | Residue |
| B | GLU28 |
| B | CSD75 |
| B | CYS78 |
| B | ARG422 |
| B | SER445 |
| B | ASP487 |
| B | PRO488 |
| B | LEU490 |
| B | GLY491 |
| B | CYS492 |
| B | ALA493 |
| B | FCO501 |
| B | NI502 |
| site_id | AH8 |
| Number of Residues | 13 |
| Details | binding site for residues H2S B 504 and SEC B 489 |
| Chain | Residue |
| B | GLU28 |
| B | CSD75 |
| B | CYS78 |
| B | ARG422 |
| B | SER445 |
| B | ASP487 |
| B | PRO488 |
| B | LEU490 |
| B | GLY491 |
| B | CYS492 |
| B | ALA493 |
| B | FCO501 |
| B | NI502 |
| site_id | AH9 |
| Number of Residues | 12 |
| Details | binding site for residues H2S D 504 and SEC D 489 |
| Chain | Residue |
| D | GLU28 |
| D | CSD75 |
| D | CYS78 |
| D | ARG422 |
| D | SER445 |
| D | PRO488 |
| D | LEU490 |
| D | GLY491 |
| D | CYS492 |
| D | ALA493 |
| D | FCO501 |
| D | NI502 |
| site_id | AI1 |
| Number of Residues | 12 |
| Details | binding site for residues H2S D 504 and SEC D 489 |
| Chain | Residue |
| D | GLU28 |
| D | CSD75 |
| D | CYS78 |
| D | ARG422 |
| D | SER445 |
| D | PRO488 |
| D | LEU490 |
| D | GLY491 |
| D | CYS492 |
| D | ALA493 |
| D | FCO501 |
| D | NI502 |
Functional Information from PROSITE/UniProt
| site_id | PS00507 |
| Number of Residues | 26 |
| Details | NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGFEtilrgrdprdasqivQRiCGVC |
| Chain | Residue | Details |
| B | ARG53-CYS78 |
| site_id | PS00508 |
| Number of Residues | 10 |
| Details | NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPULGCav.H |
| Chain | Residue | Details |
| B | PHE486-HIS495 |
