3VD3
E. coli (lacZ) beta-galactosidase (N460D)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| A | 0004565 | molecular_function | beta-galactosidase activity |
| A | 0005975 | biological_process | carbohydrate metabolic process |
| A | 0005990 | biological_process | lactose catabolic process |
| A | 0009341 | cellular_component | beta-galactosidase complex |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| A | 0030246 | molecular_function | carbohydrate binding |
| A | 0031420 | molecular_function | alkali metal ion binding |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| B | 0004565 | molecular_function | beta-galactosidase activity |
| B | 0005975 | biological_process | carbohydrate metabolic process |
| B | 0005990 | biological_process | lactose catabolic process |
| B | 0009341 | cellular_component | beta-galactosidase complex |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| B | 0030246 | molecular_function | carbohydrate binding |
| B | 0031420 | molecular_function | alkali metal ion binding |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| C | 0004565 | molecular_function | beta-galactosidase activity |
| C | 0005975 | biological_process | carbohydrate metabolic process |
| C | 0005990 | biological_process | lactose catabolic process |
| C | 0009341 | cellular_component | beta-galactosidase complex |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| C | 0030246 | molecular_function | carbohydrate binding |
| C | 0031420 | molecular_function | alkali metal ion binding |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| D | 0004565 | molecular_function | beta-galactosidase activity |
| D | 0005975 | biological_process | carbohydrate metabolic process |
| D | 0005990 | biological_process | lactose catabolic process |
| D | 0009341 | cellular_component | beta-galactosidase complex |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| D | 0030246 | molecular_function | carbohydrate binding |
| D | 0031420 | molecular_function | alkali metal ion binding |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 3001 |
| Chain | Residue |
| A | GLU416 |
| A | HIS418 |
| A | GLU461 |
| A | HOH4007 |
| A | HOH4111 |
| A | HOH4112 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 3101 |
| Chain | Residue |
| A | ASN604 |
| A | HOH4097 |
| A | HOH4099 |
| A | TYR100 |
| A | ASP201 |
| A | PHE601 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA A 3102 |
| Chain | Residue |
| A | PHE556 |
| A | TYR559 |
| A | PRO560 |
| A | LEU562 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 3103 |
| Chain | Residue |
| A | PHE931 |
| A | PRO932 |
| A | LEU967 |
| A | MET968 |
| A | THR970 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE DMS A 8001 |
| Chain | Residue |
| A | THR229 |
| A | VAL330 |
| A | GLY331 |
| A | ARG333 |
| A | ASN449 |
| A | PRO451 |
| A | ARG482 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS A 8002 |
| Chain | Residue |
| A | ARG557 |
| A | HIS622 |
| A | GLN623 |
| A | GLN628 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS A 8003 |
| Chain | Residue |
| A | LYS380 |
| A | ASN383 |
| A | PHE626 |
| A | TYR642 |
| A | TRP708 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS A 8004 |
| Chain | Residue |
| A | THR271 |
| A | LEU291 |
| A | ARG292 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE DMS A 8005 |
| Chain | Residue |
| A | ARG505 |
| A | GLU508 |
| A | PRO1001 |
| A | SER1002 |
| A | VAL1003 |
| A | HOH4023 |
| A | HOH4057 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS A 8006 |
| Chain | Residue |
| A | GLU334 |
| A | VAL335 |
| A | ARG336 |
| A | PRO480 |
| A | SER481 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS A 8007 |
| Chain | Residue |
| A | PRO584 |
| A | SER586 |
| A | ARG973 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS A 8008 |
| Chain | Residue |
| A | HIS93 |
| A | GLY94 |
| A | TYR95 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE DMS A 8009 |
| Chain | Residue |
| A | TRP36 |
| A | ASP45 |
| site_id | BC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS A 8010 |
| Chain | Residue |
| A | GLN266 |
| A | VAL267 |
| A | ALA268 |
| A | SER269 |
| site_id | BC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE DMS A 8011 |
| Chain | Residue |
| A | TRP999 |
| site_id | BC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE DMS A 8012 |
| Chain | Residue |
| A | VAL85 |
| A | HIS93 |
| site_id | BC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 3001 |
| Chain | Residue |
| B | GLU416 |
| B | HIS418 |
| B | GLU461 |
| B | HOH4108 |
| B | HOH4109 |
| B | HOH4110 |
| site_id | BC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 3002 |
| Chain | Residue |
| B | ASP15 |
| B | ASN18 |
| B | VAL21 |
| B | TYR161 |
| B | GLN163 |
| B | ASP193 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA B 3101 |
| Chain | Residue |
| B | TYR100 |
| B | ASP201 |
| B | PHE601 |
| B | ASN604 |
| B | HOH4034 |
| B | HOH4086 |
| site_id | CC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 3102 |
| Chain | Residue |
| B | PHE556 |
| B | TYR559 |
| B | PRO560 |
| B | LEU562 |
| B | HOH4082 |
| site_id | CC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA B 3103 |
| Chain | Residue |
| B | PHE931 |
| B | PRO932 |
| B | LEU967 |
| B | MET968 |
| B | THR970 |
| B | HOH4050 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 3104 |
| Chain | Residue |
| B | HOH4087 |
| B | HOH4088 |
| B | SER647 |
| B | GLU650 |
| B | LEU670 |
| site_id | CC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS B 8001 |
| Chain | Residue |
| B | THR229 |
| B | GLY331 |
| B | ARG333 |
| B | ASN449 |
| B | PRO451 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS B 8002 |
| Chain | Residue |
| B | LYS380 |
| B | ASN383 |
| B | PHE384 |
| B | PHE626 |
| B | TYR642 |
| B | TRP708 |
| site_id | CC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE DMS B 8003 |
| Chain | Residue |
| B | LEU291 |
| B | ARG292 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS B 8004 |
| Chain | Residue |
| B | ARG505 |
| B | GLU508 |
| B | PRO1001 |
| B | VAL1003 |
| site_id | CC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE DMS B 8005 |
| Chain | Residue |
| B | LEU54 |
| B | ASN55 |
| site_id | DC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS B 8006 |
| Chain | Residue |
| B | GLU334 |
| B | VAL335 |
| B | ARG336 |
| B | PRO480 |
| B | HOH4013 |
| B | HOH4043 |
| site_id | DC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS B 8007 |
| Chain | Residue |
| B | ILE576 |
| B | PRO584 |
| B | TRP585 |
| B | SER586 |
| B | ARG973 |
| site_id | DC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS B 8008 |
| Chain | Residue |
| B | ASP428 |
| B | PRO430 |
| C | TRP474 |
| C | VAL478 |
| site_id | DC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS B 8009 |
| Chain | Residue |
| B | HIS93 |
| B | GLY94 |
| B | TYR95 |
| site_id | DC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS B 8010 |
| Chain | Residue |
| B | ASP45 |
| B | PRO47 |
| B | SER48 |
| site_id | DC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS B 8011 |
| Chain | Residue |
| B | GLU57 |
| B | TRP58 |
| B | ARG59 |
| B | LEU125 |
| B | THR126 |
| site_id | DC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 3001 |
| Chain | Residue |
| C | GLU416 |
| C | HIS418 |
| C | GLU461 |
| C | HOH4096 |
| C | HOH4097 |
| C | HOH4098 |
| site_id | DC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG C 3002 |
| Chain | Residue |
| C | ASP15 |
| C | ASN18 |
| C | VAL21 |
| C | GLN163 |
| C | ASP193 |
| site_id | DC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA C 3101 |
| Chain | Residue |
| C | ASP201 |
| C | PHE601 |
| C | ASN604 |
| C | HOH4084 |
| site_id | EC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA C 3102 |
| Chain | Residue |
| C | PHE556 |
| C | TYR559 |
| C | PRO560 |
| C | LEU562 |
| C | HOH4085 |
| site_id | EC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE NA C 3105 |
| Chain | Residue |
| C | ASN597 |
| site_id | EC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS C 8001 |
| Chain | Residue |
| C | VAL227 |
| C | VAL330 |
| C | GLY331 |
| C | ARG333 |
| C | ASN449 |
| C | PRO451 |
| site_id | EC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS C 8002 |
| Chain | Residue |
| C | LYS380 |
| C | ASN383 |
| C | PHE626 |
| C | TYR642 |
| C | TRP708 |
| C | HOH4018 |
| site_id | EC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS C 8003 |
| Chain | Residue |
| C | PRO32 |
| C | TRP36 |
| C | ASP45 |
| C | ALA327 |
| C | DMS8011 |
| site_id | EC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS C 8004 |
| Chain | Residue |
| C | GLY270 |
| C | LEU291 |
| C | ARG292 |
| site_id | EC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS C 8005 |
| Chain | Residue |
| C | ARG505 |
| C | GLU508 |
| C | PRO1001 |
| C | VAL1003 |
| site_id | EC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE DMS C 8006 |
| Chain | Residue |
| C | GLU334 |
| C | ARG336 |
| site_id | EC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE DMS C 8007 |
| Chain | Residue |
| C | GLU181 |
| site_id | FC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS C 8008 |
| Chain | Residue |
| C | ILE576 |
| C | PRO584 |
| C | TRP585 |
| C | SER586 |
| C | ARG973 |
| site_id | FC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS C 8009 |
| Chain | Residue |
| C | GLY275 |
| C | VAL289 |
| C | THR290 |
| C | ARG292 |
| site_id | FC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS C 8010 |
| Chain | Residue |
| B | TRP474 |
| C | ASP428 |
| C | PRO430 |
| site_id | FC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS C 8011 |
| Chain | Residue |
| C | ASP45 |
| C | ARG46 |
| C | PRO47 |
| C | SER48 |
| C | DMS8003 |
| site_id | FC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE DMS C 8012 |
| Chain | Residue |
| C | ASN55 |
| site_id | FC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 3001 |
| Chain | Residue |
| D | GLU416 |
| D | HIS418 |
| D | GLU461 |
| D | HOH4094 |
| D | HOH4104 |
| D | HOH4105 |
| site_id | FC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG D 3002 |
| Chain | Residue |
| D | ASP15 |
| D | ASN18 |
| D | VAL21 |
| D | GLN163 |
| D | ASP193 |
| site_id | FC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA D 3101 |
| Chain | Residue |
| D | TYR100 |
| D | ASP201 |
| D | PHE601 |
| D | ASN604 |
| D | HOH4095 |
| site_id | FC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 3102 |
| Chain | Residue |
| D | PHE556 |
| D | TYR559 |
| D | PRO560 |
| D | LEU562 |
| site_id | GC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE DMS D 8001 |
| Chain | Residue |
| D | THR229 |
| D | VAL330 |
| D | GLY331 |
| D | ARG333 |
| D | ASN449 |
| D | HIS450 |
| D | PRO451 |
| D | ARG482 |
| site_id | GC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS D 8002 |
| Chain | Residue |
| D | ARG557 |
| D | HIS622 |
| D | GLN623 |
| D | GLN625 |
| D | GLN628 |
| site_id | GC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS D 8003 |
| Chain | Residue |
| D | LYS380 |
| D | PHE384 |
| D | PHE626 |
| D | TYR642 |
| D | TRP708 |
| D | HOH4007 |
| site_id | GC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS D 8004 |
| Chain | Residue |
| D | GLY270 |
| D | THR271 |
| D | LEU291 |
| D | ARG292 |
| D | HOH4048 |
| site_id | GC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS D 8005 |
| Chain | Residue |
| D | ARG505 |
| D | GLU508 |
| D | PRO1001 |
| site_id | GC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS D 8006 |
| Chain | Residue |
| D | LEU54 |
| D | ASN55 |
| D | GLY56 |
| site_id | GC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS D 8007 |
| Chain | Residue |
| D | GLU334 |
| D | VAL335 |
| D | ARG336 |
| D | PRO480 |
| D | HOH4068 |
| site_id | GC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS D 8008 |
| Chain | Residue |
| D | ILE576 |
| D | PRO584 |
| D | TRP585 |
| D | SER586 |
| D | ARG973 |
| site_id | GC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS D 8009 |
| Chain | Residue |
| D | GLY275 |
| D | VAL289 |
| D | THR290 |
Functional Information from PROSITE/UniProt
| site_id | PS00719 |
| Number of Residues | 26 |
| Details | GLYCOSYL_HYDROL_F2_1 Glycosyl hydrolases family 2 signature 1. NaVRCSHYPnhplWYtlcDryGLYVV |
| Chain | Residue | Details |
| A | ASN385-VAL410 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000269|PubMed:6420154 |
| Chain | Residue | Details |
| A | GLU461 | |
| B | GLU461 | |
| C | GLU461 | |
| D | GLU461 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:1350782 |
| Chain | Residue | Details |
| A | GLU537 | |
| B | GLU537 | |
| C | GLU537 | |
| D | GLU537 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 28 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ASN102 | |
| B | GLU461 | |
| B | GLU537 | |
| B | PHE601 | |
| B | ASN604 | |
| B | TRP999 | |
| C | ASN102 | |
| C | ASP201 | |
| C | GLU461 | |
| C | GLU537 | |
| C | PHE601 | |
| A | ASP201 | |
| C | ASN604 | |
| C | TRP999 | |
| D | ASN102 | |
| D | ASP201 | |
| D | GLU461 | |
| D | GLU537 | |
| D | PHE601 | |
| D | ASN604 | |
| D | TRP999 | |
| A | GLU461 | |
| A | GLU537 | |
| A | PHE601 | |
| A | ASN604 | |
| A | TRP999 | |
| B | ASN102 | |
| B | ASP201 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11045615 |
| Chain | Residue | Details |
| A | GLU416 | |
| D | GLU416 | |
| D | HIS418 | |
| D | ASN597 | |
| A | HIS418 | |
| A | ASN597 | |
| B | GLU416 | |
| B | HIS418 | |
| B | ASN597 | |
| C | GLU416 | |
| C | HIS418 | |
| C | ASN597 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | SITE: Transition state stabilizer |
| Chain | Residue | Details |
| A | HIS357 | |
| A | HIS391 | |
| B | HIS357 | |
| B | HIS391 | |
| C | HIS357 | |
| C | HIS391 | |
| D | HIS357 | |
| D | HIS391 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | SITE: Important for ensuring that an appropriate proportion of lactose is converted to allolactose |
| Chain | Residue | Details |
| A | TRP999 | |
| B | TRP999 | |
| C | TRP999 | |
| D | TRP999 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| A | ASP201 | |
| A | ASN604 | |
| A | HIS357 | |
| A | HIS391 | |
| A | GLU416 | |
| A | HIS418 | |
| A | GLU461 | |
| A | GLU537 | |
| A | ASN597 | |
| A | PHE601 |
| site_id | MCSA2 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| B | ASP201 | |
| B | ASN604 | |
| B | HIS357 | |
| B | HIS391 | |
| B | GLU416 | |
| B | HIS418 | |
| B | GLU461 | |
| B | GLU537 | |
| B | ASN597 | |
| B | PHE601 |
| site_id | MCSA3 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| C | ASP201 | |
| C | ASN604 | |
| C | HIS357 | |
| C | HIS391 | |
| C | GLU416 | |
| C | HIS418 | |
| C | GLU461 | |
| C | GLU537 | |
| C | ASN597 | |
| C | PHE601 |
| site_id | MCSA4 |
| Number of Residues | 10 |
| Details | M-CSA 422 |
| Chain | Residue | Details |
| D | ASP201 | |
| D | ASN604 | |
| D | HIS357 | |
| D | HIS391 | |
| D | GLU416 | |
| D | HIS418 | |
| D | GLU461 | |
| D | GLU537 | |
| D | ASN597 | |
| D | PHE601 |
