2DGM
Crystal structure of Escherichia coli GadB in complex with iodide
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004351 | molecular_function | glutamate decarboxylase activity |
A | 0005515 | molecular_function | protein binding |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0006536 | biological_process | glutamate metabolic process |
A | 0006538 | biological_process | glutamate catabolic process |
A | 0016020 | cellular_component | membrane |
A | 0016830 | molecular_function | carbon-carbon lyase activity |
A | 0016831 | molecular_function | carboxy-lyase activity |
A | 0019752 | biological_process | carboxylic acid metabolic process |
A | 0030170 | molecular_function | pyridoxal phosphate binding |
A | 0051454 | biological_process | intracellular pH elevation |
B | 0004351 | molecular_function | glutamate decarboxylase activity |
B | 0005515 | molecular_function | protein binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0006536 | biological_process | glutamate metabolic process |
B | 0006538 | biological_process | glutamate catabolic process |
B | 0016020 | cellular_component | membrane |
B | 0016830 | molecular_function | carbon-carbon lyase activity |
B | 0016831 | molecular_function | carboxy-lyase activity |
B | 0019752 | biological_process | carboxylic acid metabolic process |
B | 0030170 | molecular_function | pyridoxal phosphate binding |
B | 0051454 | biological_process | intracellular pH elevation |
C | 0004351 | molecular_function | glutamate decarboxylase activity |
C | 0005515 | molecular_function | protein binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0006536 | biological_process | glutamate metabolic process |
C | 0006538 | biological_process | glutamate catabolic process |
C | 0016020 | cellular_component | membrane |
C | 0016830 | molecular_function | carbon-carbon lyase activity |
C | 0016831 | molecular_function | carboxy-lyase activity |
C | 0019752 | biological_process | carboxylic acid metabolic process |
C | 0030170 | molecular_function | pyridoxal phosphate binding |
C | 0051454 | biological_process | intracellular pH elevation |
D | 0004351 | molecular_function | glutamate decarboxylase activity |
D | 0005515 | molecular_function | protein binding |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0006536 | biological_process | glutamate metabolic process |
D | 0006538 | biological_process | glutamate catabolic process |
D | 0016020 | cellular_component | membrane |
D | 0016830 | molecular_function | carbon-carbon lyase activity |
D | 0016831 | molecular_function | carboxy-lyase activity |
D | 0019752 | biological_process | carboxylic acid metabolic process |
D | 0030170 | molecular_function | pyridoxal phosphate binding |
D | 0051454 | biological_process | intracellular pH elevation |
E | 0004351 | molecular_function | glutamate decarboxylase activity |
E | 0005515 | molecular_function | protein binding |
E | 0005737 | cellular_component | cytoplasm |
E | 0005829 | cellular_component | cytosol |
E | 0006536 | biological_process | glutamate metabolic process |
E | 0006538 | biological_process | glutamate catabolic process |
E | 0016020 | cellular_component | membrane |
E | 0016830 | molecular_function | carbon-carbon lyase activity |
E | 0016831 | molecular_function | carboxy-lyase activity |
E | 0019752 | biological_process | carboxylic acid metabolic process |
E | 0030170 | molecular_function | pyridoxal phosphate binding |
E | 0051454 | biological_process | intracellular pH elevation |
F | 0004351 | molecular_function | glutamate decarboxylase activity |
F | 0005515 | molecular_function | protein binding |
F | 0005737 | cellular_component | cytoplasm |
F | 0005829 | cellular_component | cytosol |
F | 0006536 | biological_process | glutamate metabolic process |
F | 0006538 | biological_process | glutamate catabolic process |
F | 0016020 | cellular_component | membrane |
F | 0016830 | molecular_function | carbon-carbon lyase activity |
F | 0016831 | molecular_function | carboxy-lyase activity |
F | 0019752 | biological_process | carboxylic acid metabolic process |
F | 0030170 | molecular_function | pyridoxal phosphate binding |
F | 0051454 | biological_process | intracellular pH elevation |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD A 2331 |
Chain | Residue |
A | SER16 |
F | ARG427 |
site_id | AC2 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD B 2332 |
Chain | Residue |
B | SER16 |
C | ARG427 |
site_id | AC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD B 2333 |
Chain | Residue |
B | ARG427 |
C | SER16 |
site_id | AC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD D 2334 |
Chain | Residue |
D | SER16 |
E | ARG427 |
site_id | AC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD E 2335 |
Chain | Residue |
E | SER16 |
D | ARG427 |
site_id | AC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD F 2336 |
Chain | Residue |
A | ARG427 |
F | SER16 |
site_id | AC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD A 2337 |
Chain | Residue |
A | LYS381 |
A | ILE418 |
site_id | AC8 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE IOD B 2338 |
Chain | Residue |
B | ILE418 |
site_id | AC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD C 2339 |
Chain | Residue |
C | LYS381 |
C | ILE418 |
site_id | BC1 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE IOD F 2342 |
Chain | Residue |
F | ILE418 |
site_id | BC2 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE IOD A 2343 |
Chain | Residue |
A | LYS453 |
site_id | BC3 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE IOD D 2346 |
Chain | Residue |
D | LYS453 |
site_id | BC4 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE IOD E 2347 |
Chain | Residue |
E | HIS451 |
site_id | BC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE IOD F 2348 |
Chain | Residue |
F | LYS453 |
site_id | BC6 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD A 2349 |
Chain | Residue |
A | TRP67 |
A | HIS73 |
site_id | BC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE IOD B 2350 |
Chain | Residue |
A | ASN81 |
B | ASP68 |
B | HIS73 |
site_id | BC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE IOD C 2351 |
Chain | Residue |
C | TRP67 |
C | ASP68 |
C | HIS73 |
D | ASN81 |
site_id | BC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE IOD D 2352 |
Chain | Residue |
C | ASN81 |
D | ASP68 |
D | HIS73 |
site_id | CC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE IOD E 2353 |
Chain | Residue |
E | TRP67 |
E | ASP68 |
E | HIS73 |
F | ASN81 |
site_id | CC2 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE IOD F 2354 |
Chain | Residue |
F | HIS73 |
site_id | CC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE IOD A 2355 |
Chain | Residue |
A | LEU382 |
A | THR391 |
A | LEU392 |
site_id | CC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE IOD B 2356 |
Chain | Residue |
B | LEU382 |
B | THR391 |
B | LEU392 |
site_id | CC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE IOD C 2357 |
Chain | Residue |
C | LEU382 |
C | THR391 |
C | LEU392 |
site_id | CC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE IOD D 2358 |
Chain | Residue |
D | LEU382 |
D | THR391 |
D | LEU392 |
site_id | CC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD E 2359 |
Chain | Residue |
E | THR391 |
E | LEU392 |
site_id | CC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE IOD F 2360 |
Chain | Residue |
F | THR391 |
F | LEU392 |
site_id | CC9 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP A 500 |
Chain | Residue |
A | GLY125 |
A | SER126 |
A | SER127 |
A | GLN163 |
A | THR208 |
A | THR212 |
A | ASP243 |
A | ALA245 |
A | SER273 |
A | HIS275 |
A | LYS276 |
A | HOH2651 |
B | PHE317 |
B | SER318 |
B | HOH2680 |
site_id | DC1 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP B 500 |
Chain | Residue |
A | PHE317 |
A | SER318 |
A | HOH2637 |
B | GLY125 |
B | SER126 |
B | SER127 |
B | GLN163 |
B | CYS165 |
B | THR212 |
B | ASP243 |
B | ALA245 |
B | SER273 |
B | HIS275 |
B | LYS276 |
B | HOH2703 |
site_id | DC2 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP C 501 |
Chain | Residue |
D | HOH2673 |
C | GLY125 |
C | SER126 |
C | SER127 |
C | GLN163 |
C | THR208 |
C | THR212 |
C | ASP243 |
C | ALA245 |
C | SER273 |
C | HIS275 |
C | LYS276 |
C | HOH2619 |
D | PHE317 |
D | SER318 |
site_id | DC3 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP D 501 |
Chain | Residue |
C | PHE317 |
C | SER318 |
C | HOH2649 |
D | GLY125 |
D | SER126 |
D | SER127 |
D | GLN163 |
D | CYS165 |
D | THR212 |
D | ASP243 |
D | ALA245 |
D | SER273 |
D | HIS275 |
D | LYS276 |
D | HOH2649 |
site_id | DC4 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP E 502 |
Chain | Residue |
E | SER126 |
E | SER127 |
E | GLN163 |
E | CYS165 |
E | THR208 |
E | THR212 |
E | ASP243 |
E | ALA245 |
E | SER273 |
E | HIS275 |
E | LYS276 |
E | HOH2857 |
F | PHE317 |
F | SER318 |
F | HOH2688 |
site_id | DC5 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP F 502 |
Chain | Residue |
E | PHE317 |
E | SER318 |
E | HOH2869 |
F | GLY125 |
F | SER126 |
F | SER127 |
F | GLN163 |
F | CYS165 |
F | THR212 |
F | ASP243 |
F | ALA245 |
F | SER273 |
F | HIS275 |
F | LYS276 |
F | HOH2711 |
site_id | DC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE FMT A 2550 |
Chain | Residue |
A | ASN83 |
A | ASP86 |
B | THR62 |
B | PHE63 |
site_id | DC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE FMT A 2560 |
Chain | Residue |
A | THR62 |
A | PHE63 |
B | ASN83 |
B | ASP86 |
site_id | DC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE FMT D 2570 |
Chain | Residue |
C | ASN83 |
C | ASP86 |
D | THR62 |
D | PHE63 |
site_id | DC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FMT D 2580 |
Chain | Residue |
C | THR62 |
C | PHE63 |
C | CYS64 |
D | ASN83 |
D | ASP86 |
site_id | EC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE FMT F 2590 |
Chain | Residue |
E | ASN83 |
E | ASP86 |
F | THR62 |
F | PHE63 |
site_id | EC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FMT A 2600 |
Chain | Residue |
A | TRP84 |
A | ASP97 |
A | THR121 |
A | ASN122 |
A | HOH2720 |
site_id | EC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FMT C 2610 |
Chain | Residue |
C | ASP97 |
C | LEU98 |
C | THR121 |
C | ASN122 |
C | HOH2725 |
site_id | EC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FMT E 2620 |
Chain | Residue |
E | TRP84 |
E | ASP97 |
E | THR121 |
E | ASN122 |
E | HOH2973 |
site_id | EC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE FMT D 2630 |
Chain | Residue |
D | TRP84 |
D | ASP97 |
D | LEU98 |
D | GLY120 |
D | THR121 |
D | ASN122 |
D | HOH2778 |
site_id | EC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FMT F 2640 |
Chain | Residue |
F | TRP84 |
F | ASP97 |
F | THR121 |
F | ASN122 |
F | HOH2726 |
site_id | EC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE FMT B 2650 |
Chain | Residue |
B | TRP84 |
B | ASP97 |
B | THR121 |
B | ASN122 |
B | HOH2707 |
B | HOH2848 |
site_id | EC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE FMT F 2660 |
Chain | Residue |
F | LEU98 |
F | ALA118 |
F | GLY120 |
F | GLY311 |
site_id | EC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE FMT F 2670 |
Chain | Residue |
F | PRO111 |
F | ARG290 |
F | ASP291 |
F | HOH2678 |
F | HOH2793 |
F | HOH2810 |
site_id | FC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE ACY E 2519 |
Chain | Residue |
E | THR62 |
E | PHE63 |
F | ASN83 |
F | ASP86 |
F | PHE317 |
F | SER318 |
site_id | FC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE PEG E 2833 |
Chain | Residue |
E | ASP228 |
E | ASP237 |
E | ASP239 |
E | PRO265 |
E | ARG266 |
E | LYS268 |
E | HOH2933 |
E | HOH3104 |
Functional Information from PROSITE/UniProt
site_id | PS00392 |
Number of Residues | 22 |
Details | DDC_GAD_HDC_YDC DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. SIsAsghKFGlApLGCgwVIwR |
Chain | Residue | Details |
A | SER269-ARG290 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 30 |
Details | BINDING: |
Chain | Residue | Details |
A | THR62 | |
B | HIS275 | |
C | THR62 | |
C | ASN83 | |
C | SER126 | |
C | THR212 | |
C | HIS275 | |
D | THR62 | |
D | ASN83 | |
D | SER126 | |
D | THR212 | |
A | ASN83 | |
D | HIS275 | |
E | THR62 | |
E | ASN83 | |
E | SER126 | |
E | THR212 | |
E | HIS275 | |
F | THR62 | |
F | ASN83 | |
F | SER126 | |
F | THR212 | |
A | SER126 | |
F | HIS275 | |
A | THR212 | |
A | HIS275 | |
B | THR62 | |
B | ASN83 | |
B | SER126 | |
B | THR212 |
site_id | SWS_FT_FI2 |
Number of Residues | 6 |
Details | MOD_RES: N6-(pyridoxal phosphate)lysine |
Chain | Residue | Details |
A | LYS276 | |
B | LYS276 | |
C | LYS276 | |
D | LYS276 | |
E | LYS276 | |
F | LYS276 |
site_id | SWS_FT_FI3 |
Number of Residues | 18 |
Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842 |
Chain | Residue | Details |
A | LYS446 | |
D | LYS446 | |
D | LYS453 | |
D | LYS464 | |
E | LYS446 | |
E | LYS453 | |
E | LYS464 | |
F | LYS446 | |
F | LYS453 | |
F | LYS464 | |
A | LYS453 | |
A | LYS464 | |
B | LYS446 | |
B | LYS453 | |
B | LYS464 | |
C | LYS446 | |
C | LYS453 | |
C | LYS464 |