3K2B
Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0006006 | biological_process | glucose metabolic process |
A | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
A | 0050661 | molecular_function | NADP binding |
A | 0051287 | molecular_function | NAD binding |
B | 0006006 | biological_process | glucose metabolic process |
B | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
B | 0050661 | molecular_function | NADP binding |
B | 0051287 | molecular_function | NAD binding |
C | 0006006 | biological_process | glucose metabolic process |
C | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
C | 0050661 | molecular_function | NADP binding |
C | 0051287 | molecular_function | NAD binding |
D | 0006006 | biological_process | glucose metabolic process |
D | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
D | 0050661 | molecular_function | NADP binding |
D | 0051287 | molecular_function | NAD binding |
E | 0006006 | biological_process | glucose metabolic process |
E | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
E | 0050661 | molecular_function | NADP binding |
E | 0051287 | molecular_function | NAD binding |
F | 0006006 | biological_process | glucose metabolic process |
F | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
F | 0050661 | molecular_function | NADP binding |
F | 0051287 | molecular_function | NAD binding |
G | 0006006 | biological_process | glucose metabolic process |
G | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
G | 0050661 | molecular_function | NADP binding |
G | 0051287 | molecular_function | NAD binding |
H | 0006006 | biological_process | glucose metabolic process |
H | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
H | 0050661 | molecular_function | NADP binding |
H | 0051287 | molecular_function | NAD binding |
O | 0006006 | biological_process | glucose metabolic process |
O | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
O | 0050661 | molecular_function | NADP binding |
O | 0051287 | molecular_function | NAD binding |
Q | 0006006 | biological_process | glucose metabolic process |
Q | 0016620 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor |
Q | 0050661 | molecular_function | NADP binding |
Q | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE NAD A 335 |
Chain | Residue |
A | GLY7 |
A | THR96 |
A | GLY97 |
A | VAL98 |
A | PHE99 |
A | THR119 |
A | ALA120 |
A | CYS149 |
A | ASN313 |
A | TYR317 |
A | SO4336 |
A | PHE8 |
A | HOH343 |
A | HOH345 |
A | GLY9 |
A | ARG10 |
A | ILE11 |
A | ASP32 |
A | THR33 |
A | ARG77 |
A | GLY95 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 A 336 |
Chain | Residue |
A | THR179 |
A | ASP181 |
A | ARG195 |
A | ARG231 |
A | NAD335 |
site_id | AC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 337 |
Chain | Residue |
A | SER148 |
A | THR208 |
A | GLY209 |
A | ALA210 |
site_id | AC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 A 334 |
Chain | Residue |
A | ARG20 |
A | LYS21 |
A | HOH800 |
site_id | AC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 338 |
Chain | Residue |
A | ARG102 |
A | ASP124 |
A | HOH372 |
A | HOH373 |
site_id | AC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 339 |
Chain | Residue |
A | PHE251 |
A | ALA252 |
A | GLU253 |
A | VAL299 |
site_id | AC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 340 |
Chain | Residue |
A | GLU253 |
A | ASN256 |
A | ARG260 |
A | HOH865 |
site_id | AC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 341 |
Chain | Residue |
A | SER138 |
A | HIS139 |
A | HOH706 |
A | HOH783 |
site_id | AC9 |
Number of Residues | 18 |
Details | BINDING SITE FOR RESIDUE NAD B 335 |
Chain | Residue |
B | GLY7 |
B | PHE8 |
B | GLY9 |
B | ARG10 |
B | ILE11 |
B | ASN31 |
B | ARG77 |
B | GLY95 |
B | THR96 |
B | GLY97 |
B | PHE99 |
B | THR119 |
B | ALA120 |
B | CYS149 |
B | ASN313 |
B | TYR317 |
B | SO4336 |
B | HOH354 |
site_id | BC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 B 336 |
Chain | Residue |
B | THR179 |
B | ASP181 |
B | ARG195 |
B | NAD335 |
B | HOH874 |
site_id | BC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 B 337 |
Chain | Residue |
B | SER148 |
B | THR150 |
B | THR208 |
B | GLY209 |
B | ALA210 |
B | HOH784 |
B | HOH874 |
site_id | BC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 B 334 |
Chain | Residue |
B | ARG102 |
B | LYS122 |
B | GLY123 |
B | ASP124 |
site_id | BC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 B 338 |
Chain | Residue |
B | SER138 |
B | HIS139 |
B | ASP140 |
B | ASN331 |
site_id | BC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 B 339 |
Chain | Residue |
B | GLU253 |
B | ASN256 |
B | ARG260 |
site_id | BC6 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE NAD C 335 |
Chain | Residue |
C | THR96 |
C | GLY97 |
C | PHE99 |
C | THR119 |
C | ALA120 |
C | CYS149 |
C | ASN313 |
C | TYR317 |
C | SO4336 |
C | HOH349 |
C | HOH376 |
C | GLY7 |
C | PHE8 |
C | GLY9 |
C | ARG10 |
C | ILE11 |
C | ASP32 |
C | THR33 |
C | ARG77 |
C | GLY95 |
site_id | BC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 C 336 |
Chain | Residue |
C | THR179 |
C | ASP181 |
C | ARG231 |
C | NAD335 |
C | HOH388 |
site_id | BC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 C 337 |
Chain | Residue |
C | SER148 |
C | THR208 |
C | GLY209 |
C | ALA210 |
site_id | BC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 C 334 |
Chain | Residue |
C | SER138 |
C | HIS139 |
C | ASN331 |
site_id | CC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 C 338 |
Chain | Residue |
C | ASN256 |
C | ARG260 |
C | HOH412 |
C | HOH413 |
site_id | CC2 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE NAD D 335 |
Chain | Residue |
D | GLY7 |
D | PHE8 |
D | GLY9 |
D | ARG10 |
D | ILE11 |
D | ASP32 |
D | THR33 |
D | ASN76 |
D | ARG77 |
D | THR96 |
D | GLY97 |
D | THR119 |
D | ALA120 |
D | CYS149 |
D | ASN313 |
D | TYR317 |
D | SO4336 |
D | HOH365 |
D | HOH366 |
D | HOH377 |
site_id | CC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 D 336 |
Chain | Residue |
D | THR179 |
D | ASP181 |
D | ARG231 |
D | NAD335 |
site_id | CC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 D 337 |
Chain | Residue |
D | SER148 |
D | CYS149 |
D | THR150 |
D | THR208 |
D | ARG231 |
D | HOH399 |
site_id | CC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 D 334 |
Chain | Residue |
D | GLU253 |
D | ASN256 |
D | ARG260 |
site_id | CC6 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE NAD E 335 |
Chain | Residue |
E | GLY7 |
E | PHE8 |
E | GLY9 |
E | ARG10 |
E | ILE11 |
E | ASN31 |
E | THR33 |
E | ARG77 |
E | GLY95 |
E | THR96 |
E | GLY97 |
E | THR119 |
E | ALA120 |
E | CYS149 |
E | THR179 |
E | ASN313 |
E | GLU314 |
E | TYR317 |
E | SO4336 |
site_id | CC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 E 336 |
Chain | Residue |
E | THR179 |
E | ASP181 |
E | ARG195 |
E | ARG231 |
E | NAD335 |
site_id | CC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 E 337 |
Chain | Residue |
E | SER148 |
E | THR150 |
E | THR208 |
E | GLY209 |
E | ALA210 |
site_id | CC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 E 334 |
Chain | Residue |
E | GLU253 |
E | ASN256 |
E | ARG260 |
E | SER294 |
E | HOH536 |
site_id | DC1 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 E 338 |
Chain | Residue |
E | ASP135 |
E | ILE327 |
E | ASN331 |
site_id | DC2 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE NAD F 335 |
Chain | Residue |
F | GLY7 |
F | GLY9 |
F | ARG10 |
F | ILE11 |
F | ASP32 |
F | ARG77 |
F | GLY95 |
F | THR96 |
F | GLY97 |
F | VAL98 |
F | PHE99 |
F | THR119 |
F | ALA120 |
F | CYS149 |
F | ASN313 |
F | TYR317 |
G | SER188 |
site_id | DC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 F 336 |
Chain | Residue |
F | THR179 |
F | ASP181 |
F | ARG195 |
F | ARG231 |
site_id | DC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 F 337 |
Chain | Residue |
F | SER148 |
F | THR150 |
F | THR208 |
F | GLY209 |
F | ALA210 |
site_id | DC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 F 334 |
Chain | Residue |
F | GLU253 |
F | ASN256 |
F | ARG260 |
F | ASP275 |
site_id | DC6 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE NAD G 335 |
Chain | Residue |
G | GLY7 |
G | GLY9 |
G | ARG10 |
G | ILE11 |
G | ASP32 |
G | THR33 |
G | ARG77 |
G | THR96 |
G | GLY97 |
G | PHE99 |
G | THR119 |
G | ALA120 |
G | CYS149 |
G | THR179 |
G | ASN313 |
G | GLU314 |
G | TYR317 |
G | SO4336 |
G | HOH340 |
site_id | DC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 G 336 |
Chain | Residue |
G | THR179 |
G | ASP181 |
G | ARG195 |
G | ARG231 |
G | NAD335 |
site_id | DC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 G 337 |
Chain | Residue |
G | SER148 |
G | THR150 |
G | THR208 |
G | GLY209 |
G | ALA210 |
site_id | DC9 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 G 334 |
Chain | Residue |
G | THR127 |
G | LEU216 |
site_id | EC1 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 G 338 |
Chain | Residue |
G | SER138 |
G | HIS139 |
G | ASP140 |
site_id | EC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 G 339 |
Chain | Residue |
G | GLU253 |
G | ASN256 |
G | ARG260 |
G | HOH344 |
G | HOH652 |
site_id | EC3 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE NAD H 335 |
Chain | Residue |
E | SER188 |
H | GLY7 |
H | PHE8 |
H | GLY9 |
H | ARG10 |
H | ILE11 |
H | ASP32 |
H | THR33 |
H | ARG77 |
H | GLY95 |
H | THR96 |
H | GLY97 |
H | VAL98 |
H | THR119 |
H | ALA120 |
H | CYS149 |
H | THR179 |
H | ASN313 |
H | GLU314 |
H | TYR317 |
H | SO4336 |
site_id | EC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 H 336 |
Chain | Residue |
H | THR179 |
H | ASP181 |
H | ARG195 |
H | ARG231 |
H | NAD335 |
site_id | EC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 H 337 |
Chain | Residue |
H | SER148 |
H | THR150 |
H | SER207 |
H | THR208 |
H | ALA210 |
H | HOH861 |
H | HOH862 |
site_id | EC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 H 334 |
Chain | Residue |
H | GLU253 |
H | ASN256 |
H | ARG260 |
H | SER294 |
site_id | EC7 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE NAD O 335 |
Chain | Residue |
O | GLY7 |
O | PHE8 |
O | GLY9 |
O | ARG10 |
O | ILE11 |
O | ASP32 |
O | THR33 |
O | ARG77 |
O | GLY95 |
O | THR96 |
O | GLY97 |
O | PHE99 |
O | THR119 |
O | ALA120 |
O | ASN313 |
O | TYR317 |
O | SO4336 |
O | HOH346 |
O | HOH359 |
O | HOH362 |
O | HOH370 |
O | HOH434 |
O | HOH435 |
O | HOH436 |
O | HOH440 |
site_id | EC8 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SO4 O 336 |
Chain | Residue |
O | HOH35 |
O | THR179 |
O | ASP181 |
O | ARG195 |
O | ARG231 |
O | NAD335 |
O | HOH398 |
O | HOH415 |
site_id | EC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 O 337 |
Chain | Residue |
O | SER148 |
O | THR150 |
O | THR208 |
O | ALA210 |
O | HOH397 |
O | HOH407 |
O | HOH857 |
site_id | FC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 O 334 |
Chain | Residue |
O | GLY60 |
O | GLU61 |
O | THR62 |
O | HOH375 |
site_id | FC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 O 338 |
Chain | Residue |
O | ARG102 |
O | LYS122 |
O | GLY123 |
O | ASP124 |
site_id | FC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 O 339 |
Chain | Residue |
C | LYS122 |
O | SER138 |
O | HIS139 |
O | ASP140 |
O | LYS333 |
O | HOH409 |
site_id | FC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 O 340 |
Chain | Residue |
O | GLU253 |
O | ASN256 |
O | ARG260 |
site_id | FC5 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE NAD Q 335 |
Chain | Residue |
Q | GLY7 |
Q | PHE8 |
Q | GLY9 |
Q | ARG10 |
Q | ILE11 |
Q | ASP32 |
Q | THR33 |
Q | ARG77 |
Q | GLY95 |
Q | THR96 |
Q | GLY97 |
Q | PHE99 |
Q | THR119 |
Q | ALA120 |
Q | CYS149 |
Q | THR179 |
Q | ASN313 |
Q | TYR317 |
Q | SO4336 |
Q | HOH346 |
Q | HOH350 |
Q | HOH446 |
site_id | FC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 Q 336 |
Chain | Residue |
Q | THR179 |
Q | ASP181 |
Q | ARG195 |
Q | ARG231 |
Q | NAD335 |
site_id | FC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SO4 Q 337 |
Chain | Residue |
Q | SER148 |
Q | THR150 |
Q | THR208 |
Q | GLY209 |
Q | ALA210 |
Q | HOH467 |
Q | HOH790 |
site_id | FC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE SO4 Q 334 |
Chain | Residue |
Q | PRO126 |
Q | THR127 |
Q | TYR128 |
Q | ASN133 |
Q | LEU216 |
Q | HOH462 |
site_id | FC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 Q 338 |
Chain | Residue |
Q | PHE251 |
Q | ALA252 |
Q | VAL299 |
Q | HOH477 |
site_id | GC1 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 Q 339 |
Chain | Residue |
Q | ARG284 |
Q | HOH805 |
Functional Information from PROSITE/UniProt
site_id | PS00071 |
Number of Residues | 8 |
Details | GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNcL |
Chain | Residue | Details |
A | ALA147-LEU154 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 10 |
Details | ACT_SITE: Nucleophile => ECO:0000255|PROSITE-ProRule:PRU10009 |
Chain | Residue | Details |
A | CYS149 | |
Q | CYS149 | |
B | CYS149 | |
C | CYS149 | |
D | CYS149 | |
E | CYS149 | |
F | CYS149 | |
G | CYS149 | |
H | CYS149 | |
O | CYS149 |
site_id | SWS_FT_FI2 |
Number of Residues | 40 |
Details | BINDING: BINDING => ECO:0000269|PubMed:20516587, ECO:0000269|PubMed:22514274 |
Chain | Residue | Details |
A | ARG10 | |
C | ASP32 | |
C | ARG77 | |
C | ASN313 | |
D | ARG10 | |
D | ASP32 | |
D | ARG77 | |
D | ASN313 | |
E | ARG10 | |
E | ASP32 | |
E | ARG77 | |
A | ASP32 | |
E | ASN313 | |
F | ARG10 | |
F | ASP32 | |
F | ARG77 | |
F | ASN313 | |
G | ARG10 | |
G | ASP32 | |
G | ARG77 | |
G | ASN313 | |
H | ARG10 | |
A | ARG77 | |
H | ASP32 | |
H | ARG77 | |
H | ASN313 | |
O | ARG10 | |
O | ASP32 | |
O | ARG77 | |
O | ASN313 | |
Q | ARG10 | |
Q | ASP32 | |
Q | ARG77 | |
A | ASN313 | |
Q | ASN313 | |
B | ARG10 | |
B | ASP32 | |
B | ARG77 | |
B | ASN313 | |
C | ARG10 |
site_id | SWS_FT_FI3 |
Number of Residues | 50 |
Details | BINDING: BINDING => ECO:0000250 |
Chain | Residue | Details |
A | SER148 | |
B | ARG231 | |
C | SER148 | |
C | THR179 | |
C | ARG195 | |
C | THR208 | |
C | ARG231 | |
D | SER148 | |
D | THR179 | |
D | ARG195 | |
D | THR208 | |
A | THR179 | |
D | ARG231 | |
E | SER148 | |
E | THR179 | |
E | ARG195 | |
E | THR208 | |
E | ARG231 | |
F | SER148 | |
F | THR179 | |
F | ARG195 | |
F | THR208 | |
A | ARG195 | |
F | ARG231 | |
G | SER148 | |
G | THR179 | |
G | ARG195 | |
G | THR208 | |
G | ARG231 | |
H | SER148 | |
H | THR179 | |
H | ARG195 | |
H | THR208 | |
A | THR208 | |
H | ARG231 | |
O | SER148 | |
O | THR179 | |
O | ARG195 | |
O | THR208 | |
O | ARG231 | |
Q | SER148 | |
Q | THR179 | |
Q | ARG195 | |
Q | THR208 | |
A | ARG231 | |
Q | ARG231 | |
B | SER148 | |
B | THR179 | |
B | ARG195 | |
B | THR208 |
site_id | SWS_FT_FI4 |
Number of Residues | 10 |
Details | SITE: Activates thiol group during catalysis => ECO:0000250 |
Chain | Residue | Details |
A | HIS176 | |
Q | HIS176 | |
B | HIS176 | |
C | HIS176 | |
D | HIS176 | |
E | HIS176 | |
F | HIS176 | |
G | HIS176 | |
H | HIS176 | |
O | HIS176 |