Research workbench
Crystal structure of the complex of human lactoferrin N-lobe and lactoferrin-binding domain of pneumococcal surface protein a
Analyse Crystal structure of the complex of human lactoferrin N-lobe and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PMS
- Type
- protein
- Length
- 880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactotransferrin; Pneumococcal surface protein a (pspa)
- EC
- 3.4.21.-
- UniProt
- Q5EK51, Q8DRI0
- Ligands
- NAG, FE, ZN, SO4, CO3
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lactotransferrin (EC 3.4.21.-) | protein | 331 | 35% helix, 21% strand | Q5EK51 |
| C, D | Pneumococcal surface protein a (pspa) | protein | 109 | 82% helix, 0% strand | Q8DRI0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains C, A, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.78 | 0.90 | 40 | empty |
| 2 | 1038 | 0.78 | 0.80 | 99 | SO4 |
| 3 | 747 | 0.75 | 0.80 | 80 | empty |
| 4 | 358 | 0.67 | 0.81 | 51 | empty |
| 5 | 51 | 0.34 | 0.78 | 11 | empty |
Interfaces
4 interfaces between chains.
- B–D · 986 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 980 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 365 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2PMS · Crystal structure of the complex of human lactoferrin N-lobe and lactoferrin-binding… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5EK51
- Every structure of UniProt Q8DRI0
- Elsewhere: RCSB PDB 2PMS · PDBe 2PMS · UniProt Q5EK51 · UniProt Q8DRI0
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