3AXM
Structure of rice Rubisco in complex with 6PG
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0004497 | molecular_function | monooxygenase activity |
| A | 0009507 | cellular_component | chloroplast |
| A | 0009536 | cellular_component | plastid |
| A | 0009853 | biological_process | photorespiration |
| A | 0015977 | biological_process | carbon fixation |
| A | 0015979 | biological_process | photosynthesis |
| A | 0016829 | molecular_function | lyase activity |
| A | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| A | 0019253 | biological_process | reductive pentose-phosphate cycle |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004497 | molecular_function | monooxygenase activity |
| B | 0009507 | cellular_component | chloroplast |
| B | 0009536 | cellular_component | plastid |
| B | 0009853 | biological_process | photorespiration |
| B | 0015977 | biological_process | carbon fixation |
| B | 0015979 | biological_process | photosynthesis |
| B | 0016829 | molecular_function | lyase activity |
| B | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| B | 0019253 | biological_process | reductive pentose-phosphate cycle |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0004497 | molecular_function | monooxygenase activity |
| C | 0009507 | cellular_component | chloroplast |
| C | 0009536 | cellular_component | plastid |
| C | 0009853 | biological_process | photorespiration |
| C | 0015977 | biological_process | carbon fixation |
| C | 0015979 | biological_process | photosynthesis |
| C | 0016829 | molecular_function | lyase activity |
| C | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| C | 0019253 | biological_process | reductive pentose-phosphate cycle |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0004497 | molecular_function | monooxygenase activity |
| D | 0009507 | cellular_component | chloroplast |
| D | 0009536 | cellular_component | plastid |
| D | 0009853 | biological_process | photorespiration |
| D | 0015977 | biological_process | carbon fixation |
| D | 0015979 | biological_process | photosynthesis |
| D | 0016829 | molecular_function | lyase activity |
| D | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| D | 0019253 | biological_process | reductive pentose-phosphate cycle |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0000166 | molecular_function | nucleotide binding |
| E | 0000287 | molecular_function | magnesium ion binding |
| E | 0004497 | molecular_function | monooxygenase activity |
| E | 0009507 | cellular_component | chloroplast |
| E | 0009536 | cellular_component | plastid |
| E | 0009853 | biological_process | photorespiration |
| E | 0015977 | biological_process | carbon fixation |
| E | 0015979 | biological_process | photosynthesis |
| E | 0016829 | molecular_function | lyase activity |
| E | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| E | 0019253 | biological_process | reductive pentose-phosphate cycle |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0000166 | molecular_function | nucleotide binding |
| F | 0000287 | molecular_function | magnesium ion binding |
| F | 0004497 | molecular_function | monooxygenase activity |
| F | 0009507 | cellular_component | chloroplast |
| F | 0009536 | cellular_component | plastid |
| F | 0009853 | biological_process | photorespiration |
| F | 0015977 | biological_process | carbon fixation |
| F | 0015979 | biological_process | photosynthesis |
| F | 0016829 | molecular_function | lyase activity |
| F | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| F | 0019253 | biological_process | reductive pentose-phosphate cycle |
| F | 0046872 | molecular_function | metal ion binding |
| G | 0000166 | molecular_function | nucleotide binding |
| G | 0000287 | molecular_function | magnesium ion binding |
| G | 0004497 | molecular_function | monooxygenase activity |
| G | 0009507 | cellular_component | chloroplast |
| G | 0009536 | cellular_component | plastid |
| G | 0009853 | biological_process | photorespiration |
| G | 0015977 | biological_process | carbon fixation |
| G | 0015979 | biological_process | photosynthesis |
| G | 0016829 | molecular_function | lyase activity |
| G | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| G | 0019253 | biological_process | reductive pentose-phosphate cycle |
| G | 0046872 | molecular_function | metal ion binding |
| H | 0000166 | molecular_function | nucleotide binding |
| H | 0000287 | molecular_function | magnesium ion binding |
| H | 0004497 | molecular_function | monooxygenase activity |
| H | 0009507 | cellular_component | chloroplast |
| H | 0009536 | cellular_component | plastid |
| H | 0009853 | biological_process | photorespiration |
| H | 0015977 | biological_process | carbon fixation |
| H | 0015979 | biological_process | photosynthesis |
| H | 0016829 | molecular_function | lyase activity |
| H | 0016984 | molecular_function | ribulose-bisphosphate carboxylase activity |
| H | 0019253 | biological_process | reductive pentose-phosphate cycle |
| H | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 478 |
| Chain | Residue |
| A | KCX201 |
| A | ASP203 |
| A | GLU204 |
| A | 6PG479 |
| A | HOH2934 |
| site_id | AC2 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE 6PG A 479 |
| Chain | Residue |
| A | GLU204 |
| A | HIS294 |
| A | ARG295 |
| A | HIS298 |
| A | SER379 |
| A | MG478 |
| A | HOH497 |
| A | HOH498 |
| A | HOH884 |
| A | HOH1916 |
| A | HOH2402 |
| A | HOH2491 |
| A | HOH2648 |
| A | HOH2934 |
| A | HOH3580 |
| B | ASN123 |
| A | THR173 |
| A | LYS175 |
| A | KCX201 |
| A | ASP203 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 478 |
| Chain | Residue |
| B | KCX201 |
| B | ASP203 |
| B | GLU204 |
| B | 6PG479 |
| B | HOH2967 |
| site_id | AC4 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE 6PG B 479 |
| Chain | Residue |
| A | ASN123 |
| B | THR173 |
| B | LYS175 |
| B | KCX201 |
| B | ASP203 |
| B | GLU204 |
| B | HIS294 |
| B | ARG295 |
| B | HIS298 |
| B | SER379 |
| B | MG478 |
| B | HOH649 |
| B | HOH1425 |
| B | HOH1849 |
| B | HOH1984 |
| B | HOH2967 |
| B | HOH3286 |
| B | HOH3596 |
| B | HOH3597 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG C 478 |
| Chain | Residue |
| C | KCX201 |
| C | ASP203 |
| C | GLU204 |
| C | 6PG479 |
| C | HOH481 |
| site_id | AC6 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE 6PG C 479 |
| Chain | Residue |
| C | LYS175 |
| C | KCX201 |
| C | ASP203 |
| C | GLU204 |
| C | HIS294 |
| C | ARG295 |
| C | HIS298 |
| C | SER379 |
| C | MG478 |
| C | HOH481 |
| C | HOH695 |
| C | HOH1439 |
| C | HOH1507 |
| C | HOH1962 |
| C | HOH2485 |
| C | HOH3592 |
| D | ASN123 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG D 478 |
| Chain | Residue |
| D | KCX201 |
| D | ASP203 |
| D | GLU204 |
| D | 6PG479 |
| D | HOH3132 |
| site_id | AC8 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE 6PG D 479 |
| Chain | Residue |
| C | ASN123 |
| D | LYS175 |
| D | KCX201 |
| D | ASP203 |
| D | GLU204 |
| D | HIS294 |
| D | ARG295 |
| D | HIS298 |
| D | SER379 |
| D | MG478 |
| D | HOH1958 |
| D | HOH2156 |
| D | HOH2304 |
| D | HOH2356 |
| D | HOH3132 |
| D | HOH3437 |
| D | HOH3598 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG E 478 |
| Chain | Residue |
| E | KCX201 |
| E | ASP203 |
| E | GLU204 |
| E | 6PG479 |
| E | HOH1908 |
| site_id | BC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE 6PG E 479 |
| Chain | Residue |
| E | LYS175 |
| E | KCX201 |
| E | ASP203 |
| E | GLU204 |
| E | HIS294 |
| E | ARG295 |
| E | HIS298 |
| E | SER379 |
| E | MG478 |
| E | HOH512 |
| E | HOH794 |
| E | HOH1908 |
| E | HOH1929 |
| E | HOH2080 |
| E | HOH2752 |
| E | HOH3520 |
| F | ASN123 |
| E | THR173 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG F 478 |
| Chain | Residue |
| F | KCX201 |
| F | ASP203 |
| F | GLU204 |
| F | 6PG479 |
| F | HOH2817 |
| site_id | BC3 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE 6PG F 479 |
| Chain | Residue |
| E | ASN123 |
| E | HOH524 |
| E | HOH3356 |
| F | THR173 |
| F | LYS175 |
| F | KCX201 |
| F | ASP203 |
| F | GLU204 |
| F | HIS294 |
| F | ARG295 |
| F | HIS298 |
| F | GLY329 |
| F | SER379 |
| F | MG478 |
| F | HOH508 |
| F | HOH1401 |
| F | HOH1445 |
| F | HOH2795 |
| F | HOH2817 |
| F | HOH3601 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG G 478 |
| Chain | Residue |
| G | KCX201 |
| G | ASP203 |
| G | GLU204 |
| G | 6PG479 |
| G | HOH1909 |
| site_id | BC5 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE 6PG G 479 |
| Chain | Residue |
| G | THR173 |
| G | LYS175 |
| G | KCX201 |
| G | ASP203 |
| G | GLU204 |
| G | HIS294 |
| G | ARG295 |
| G | HIS298 |
| G | SER379 |
| G | MG478 |
| G | HOH756 |
| G | HOH1909 |
| G | HOH3396 |
| G | HOH3584 |
| G | HOH3585 |
| G | HOH3586 |
| G | HOH3588 |
| H | ASN123 |
| H | HOH3483 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG H 478 |
| Chain | Residue |
| H | KCX201 |
| H | ASP203 |
| H | GLU204 |
| H | 6PG479 |
| H | HOH3197 |
| site_id | BC7 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE 6PG H 479 |
| Chain | Residue |
| G | ASN123 |
| H | THR173 |
| H | LYS175 |
| H | KCX201 |
| H | ASP203 |
| H | GLU204 |
| H | HIS294 |
| H | ARG295 |
| H | HIS298 |
| H | GLY329 |
| H | SER379 |
| H | MG478 |
| H | HOH522 |
| H | HOH1446 |
| H | HOH2251 |
| H | HOH3197 |
| H | HOH3314 |
| H | HOH3604 |
Functional Information from PROSITE/UniProt
| site_id | PS00157 |
| Number of Residues | 9 |
| Details | RUBISCO_LARGE Ribulose bisphosphate carboxylase large chain active site. GlDFtKdDE |
| Chain | Residue | Details |
| A | GLY196-GLU204 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 16 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255|HAMAP-Rule:MF_01338 |
| Chain | Residue | Details |
| A | LYS175 | |
| E | HIS294 | |
| F | LYS175 | |
| F | HIS294 | |
| G | LYS175 | |
| G | HIS294 | |
| H | LYS175 | |
| H | HIS294 | |
| A | HIS294 | |
| B | LYS175 | |
| B | HIS294 | |
| C | LYS175 | |
| C | HIS294 | |
| D | LYS175 | |
| D | HIS294 | |
| E | LYS175 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 48 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22609438, ECO:0007744|PDB:3AXK |
| Chain | Residue | Details |
| A | GLU60 | |
| B | LYS175 | |
| B | ARG295 | |
| B | GLY381 | |
| C | GLU60 | |
| C | THR68 | |
| C | PHE127 | |
| C | LYS175 | |
| C | ARG295 | |
| C | GLY381 | |
| D | GLU60 | |
| A | THR68 | |
| D | THR68 | |
| D | PHE127 | |
| D | LYS175 | |
| D | ARG295 | |
| D | GLY381 | |
| E | GLU60 | |
| E | THR68 | |
| E | PHE127 | |
| E | LYS175 | |
| E | ARG295 | |
| A | PHE127 | |
| E | GLY381 | |
| F | GLU60 | |
| F | THR68 | |
| F | PHE127 | |
| F | LYS175 | |
| F | ARG295 | |
| F | GLY381 | |
| G | GLU60 | |
| G | THR68 | |
| G | PHE127 | |
| A | LYS175 | |
| G | LYS175 | |
| G | ARG295 | |
| G | GLY381 | |
| H | GLU60 | |
| H | THR68 | |
| H | PHE127 | |
| H | LYS175 | |
| H | ARG295 | |
| H | GLY381 | |
| A | ARG295 | |
| A | GLY381 | |
| B | GLU60 | |
| B | THR68 | |
| B | PHE127 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 32 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22609438, ECO:0007744|PDB:1WDD |
| Chain | Residue | Details |
| A | THR65 | |
| C | THR173 | |
| C | HIS327 | |
| C | SER379 | |
| D | THR65 | |
| D | THR173 | |
| D | HIS327 | |
| D | SER379 | |
| E | THR65 | |
| E | THR173 | |
| E | HIS327 | |
| A | THR173 | |
| E | SER379 | |
| F | THR65 | |
| F | THR173 | |
| F | HIS327 | |
| F | SER379 | |
| G | THR65 | |
| G | THR173 | |
| G | HIS327 | |
| G | SER379 | |
| H | THR65 | |
| A | HIS327 | |
| H | THR173 | |
| H | HIS327 | |
| H | SER379 | |
| A | SER379 | |
| B | THR65 | |
| B | THR173 | |
| B | HIS327 | |
| B | SER379 | |
| C | THR65 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: in homodimeric partner => ECO:0000269|PubMed:22609438, ECO:0007744|PDB:1WDD, ECO:0007744|PDB:3AXM |
| Chain | Residue | Details |
| A | ASN123 | |
| B | ASN123 | |
| C | ASN123 | |
| D | ASN123 | |
| E | ASN123 | |
| F | ASN123 | |
| G | ASN123 | |
| H | ASN123 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: via carbamate group => ECO:0000269|PubMed:22609438, ECO:0007744|PDB:1WDD, ECO:0007744|PDB:3AXK, ECO:0007744|PDB:3AXM |
| Chain | Residue | Details |
| A | KCX201 | |
| B | KCX201 | |
| C | KCX201 | |
| D | KCX201 | |
| E | KCX201 | |
| F | KCX201 | |
| G | KCX201 | |
| H | KCX201 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22609438, ECO:0007744|PDB:1WDD, ECO:0007744|PDB:3AXK, ECO:0007744|PDB:3AXM |
| Chain | Residue | Details |
| A | ASP203 | |
| E | GLU204 | |
| F | ASP203 | |
| F | GLU204 | |
| G | ASP203 | |
| G | GLU204 | |
| H | ASP203 | |
| H | GLU204 | |
| A | GLU204 | |
| B | ASP203 | |
| B | GLU204 | |
| C | ASP203 | |
| C | GLU204 | |
| D | ASP203 | |
| D | GLU204 | |
| E | ASP203 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0007744|PDB:1WDD |
| Chain | Residue | Details |
| A | HIS294 | |
| E | LYS334 | |
| F | HIS294 | |
| F | LYS334 | |
| G | HIS294 | |
| G | LYS334 | |
| H | HIS294 | |
| H | LYS334 | |
| A | LYS334 | |
| B | HIS294 | |
| B | LYS334 | |
| C | HIS294 | |
| C | LYS334 | |
| D | HIS294 | |
| D | LYS334 | |
| E | HIS294 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22609438 |
| Chain | Residue | Details |
| A | GLY404 | |
| B | GLY404 | |
| C | GLY404 | |
| D | GLY404 | |
| E | GLY404 | |
| F | GLY404 | |
| G | GLY404 | |
| H | GLY404 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 8 |
| Details | SITE: Transition state stabilizer |
| Chain | Residue | Details |
| A | LYS334 | |
| B | LYS334 | |
| C | LYS334 | |
| D | LYS334 | |
| E | LYS334 | |
| F | LYS334 | |
| G | LYS334 | |
| H | LYS334 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 8 |
| Details | MOD_RES: N-acetylproline => ECO:0000250 |
| Chain | Residue | Details |
| A | PRO3 | |
| B | PRO3 | |
| C | PRO3 | |
| D | PRO3 | |
| E | PRO3 | |
| F | PRO3 | |
| G | PRO3 | |
| H | PRO3 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-carboxylysine => ECO:0000269|PubMed:22609438 |
| Chain | Residue | Details |
| A | KCX201 | |
| B | KCX201 | |
| C | KCX201 | |
| D | KCX201 | |
| E | KCX201 | |
| F | KCX201 | |
| G | KCX201 | |
| H | KCX201 |
