1CB6
STRUCTURE OF HUMAN APOLACTOFERRIN AT 2.0 A RESOLUTION.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0001503 | biological_process | ossification |
| A | 0001530 | molecular_function | lipopolysaccharide binding |
| A | 0001817 | biological_process | regulation of cytokine production |
| A | 0002227 | biological_process | innate immune response in mucosa |
| A | 0002376 | biological_process | immune system process |
| A | 0003677 | molecular_function | DNA binding |
| A | 0004252 | molecular_function | serine-type endopeptidase activity |
| A | 0004869 | molecular_function | cysteine-type endopeptidase inhibitor activity |
| A | 0005506 | molecular_function | iron ion binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005615 | cellular_component | extracellular space |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005769 | cellular_component | early endosome |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006508 | biological_process | proteolysis |
| A | 0006811 | biological_process | monoatomic ion transport |
| A | 0006826 | biological_process | iron ion transport |
| A | 0006959 | biological_process | humoral immune response |
| A | 0008201 | molecular_function | heparin binding |
| A | 0008233 | molecular_function | peptidase activity |
| A | 0008236 | molecular_function | serine-type peptidase activity |
| A | 0009986 | cellular_component | cell surface |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0019731 | biological_process | antibacterial humoral response |
| A | 0019732 | biological_process | antifungal humoral response |
| A | 0030141 | cellular_component | secretory granule |
| A | 0031640 | biological_process | killing of cells of another organism |
| A | 0031665 | biological_process | negative regulation of lipopolysaccharide-mediated signaling pathway |
| A | 0032680 | biological_process | regulation of tumor necrosis factor production |
| A | 0032780 | biological_process | negative regulation of ATP-dependent activity |
| A | 0032991 | cellular_component | protein-containing complex |
| A | 0033690 | biological_process | positive regulation of osteoblast proliferation |
| A | 0034145 | biological_process | positive regulation of toll-like receptor 4 signaling pathway |
| A | 0035580 | cellular_component | specific granule lumen |
| A | 0042581 | cellular_component | specific granule |
| A | 0042742 | biological_process | defense response to bacterium |
| A | 0043066 | biological_process | negative regulation of apoptotic process |
| A | 0043123 | biological_process | positive regulation of canonical NF-kappaB signal transduction |
| A | 0043539 | molecular_function | protein serine/threonine kinase activator activity |
| A | 0044793 | biological_process | negative regulation by host of viral process |
| A | 0045071 | biological_process | negative regulation of viral genome replication |
| A | 0045669 | biological_process | positive regulation of osteoblast differentiation |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0048525 | biological_process | negative regulation of viral process |
| A | 0050829 | biological_process | defense response to Gram-negative bacterium |
| A | 0051092 | biological_process | positive regulation of NF-kappaB transcription factor activity |
| A | 0055037 | cellular_component | recycling endosome |
| A | 0060349 | biological_process | bone morphogenesis |
| A | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0071902 | biological_process | positive regulation of protein serine/threonine kinase activity |
| A | 0097013 | cellular_component | phagocytic vesicle lumen |
| A | 0140912 | molecular_function | membrane destabilizing activity |
| A | 1900159 | biological_process | positive regulation of bone mineralization involved in bone maturation |
| A | 1900229 | biological_process | negative regulation of single-species biofilm formation in or on host organism |
| A | 1902732 | biological_process | positive regulation of chondrocyte proliferation |
| A | 1904724 | cellular_component | tertiary granule lumen |
| A | 2000308 | biological_process | negative regulation of tumor necrosis factor (ligand) superfamily member 11 production |
| A | 2001205 | biological_process | negative regulation of osteoclast development |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL A 1701 |
| Chain | Residue |
| A | ARG1121 |
| A | ALA1123 |
| A | GLY1124 |
| A | TYR1192 |
| A | THR1117 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL A 1702 |
| Chain | Residue |
| A | THR1461 |
| A | ARG1465 |
| A | GLY1468 |
| A | TYR1528 |
| A | HOH2237 |
| site_id | CLA |
| Number of Residues | 4 |
| Details | CHLORIDE ION LOCATED NEAR CARBONATE SITE IN CLOSED C LOBE, FORMING HYDROGEN BONDS WITH THR461_OG1, ARG465_NE, ARG465_NH2, GLY468_N AND TYR528_OH |
| Chain | Residue |
| A | THR1461 |
| A | ARG1465 |
| A | GLY1468 |
| A | TYR1528 |
| site_id | CLB |
| Number of Residues | 4 |
| Details | CHLORIDE ION LOCATED NEAR CARBONATE SITE IN OPEN N LOBE, FORMING HYDROGEN BONDS WITH THR117_OG1, ARG121_NE, ALA123_N AND TYR192_OH |
| Chain | Residue |
| A | THR1117 |
| A | ARG1121 |
| A | ALA1123 |
| A | TYR1192 |
Functional Information from PROSITE/UniProt
| site_id | PS00205 |
| Number of Residues | 10 |
| Details | TRANSFERRIN_LIKE_1 Transferrin-like domain signature 1. YyAVAVVKKG |
| Chain | Residue | Details |
| A | TYR1092-GLY1101 | |
| A | TYR1435-SER1444 |
| site_id | PS00206 |
| Number of Residues | 17 |
| Details | TRANSFERRIN_LIKE_2 Transferrin-like domain signature 2. YsGAFKCLrdgaGDVAF |
| Chain | Residue | Details |
| A | TYR1192-PHE1208 | |
| A | TYR1528-PHE1544 |
| site_id | PS00207 |
| Number of Residues | 31 |
| Details | TRANSFERRIN_LIKE_3 Transferrin-like domain signature 3. EYeLLCpDntrkp...VdkfkdChlArvpsHaVV |
| Chain | Residue | Details |
| A | GLU1226-VAL1256 | |
| A | ASP1570-VAL1600 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: ACT_SITE => ECO:0000305|PubMed:12535064 |
| Chain | Residue | Details |
| A | LYS1073 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | ACT_SITE: Nucleophile => ECO:0000305|PubMed:12535064 |
| Chain | Residue | Details |
| A | SER1259 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00741, ECO:0000269|PubMed:10089347, ECO:0000269|PubMed:10828980, ECO:0000269|PubMed:12450380, ECO:0000269|PubMed:15299793, ECO:0000269|PubMed:16201406, ECO:0000269|PubMed:17543335, ECO:0000269|PubMed:22900286, ECO:0000269|PubMed:8371268, ECO:0000269|PubMed:8594202, ECO:0000269|PubMed:8703903, ECO:0000269|PubMed:8931543, ECO:0000269|PubMed:9003186, ECO:0000269|Ref.72 |
| Chain | Residue | Details |
| A | ASP1060 | |
| A | TYR1092 | |
| A | TYR1192 | |
| A | HIS1253 | |
| A | ASP1395 | |
| A | TYR1435 | |
| A | TYR1528 | |
| A | HIS1597 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00741, ECO:0000269|PubMed:10089347, ECO:0000269|PubMed:10828980, ECO:0000269|PubMed:11128996, ECO:0000269|PubMed:12450380, ECO:0000269|PubMed:15299793, ECO:0000269|PubMed:1581307, ECO:0000269|PubMed:16201406, ECO:0000269|PubMed:17543335, ECO:0000269|PubMed:22900286, ECO:0000269|PubMed:8371268, ECO:0000269|PubMed:8594202, ECO:0000269|PubMed:8931543, ECO:0000269|PubMed:9003186, ECO:0000269|Ref.72 |
| Chain | Residue | Details |
| A | THR1117 | |
| A | ARG1121 | |
| A | ALA1123 | |
| A | GLY1124 | |
| A | THR1461 | |
| A | ARG1465 | |
| A | ALA1467 | |
| A | GLY1468 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | SITE: Interaction with PspA |
| Chain | Residue | Details |
| A | ARG1004 | |
| A | GLN1013 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | SITE: Important for iron binding |
| Chain | Residue | Details |
| A | ARG1210 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:15299444, ECO:0000269|PubMed:15299793, ECO:0000269|PubMed:1581307, ECO:0000269|PubMed:16201406, ECO:0000269|PubMed:18780401, ECO:0000269|PubMed:8069634, ECO:0000269|Ref.72 |
| Chain | Residue | Details |
| A | ASN1137 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:15299793, ECO:0000269|PubMed:1581307, ECO:0000269|PubMed:16201406, ECO:0000269|PubMed:18780401, ECO:0000269|PubMed:19159218, ECO:0000269|Ref.72 |
| Chain | Residue | Details |
| A | ASN1478 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:18780401 |
| Chain | Residue | Details |
| A | ASN1623 |
