Research workbench
Complex structure of human C5A and its binding repebody
Analyse Complex structure of human C5A and its binding repebody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B4P
- Type
- protein
- Length
- 658 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Repebody; C5A anaphylatoxin
- UniProt
- P01031
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Repebody | protein | 254 | 14% helix, 17% strand | — |
| B, D | C5A anaphylatoxin | protein | 72 | 63% helix, 0% strand | P01031 |
| C | Repebody | protein | 260 | 15% helix, 18% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.77 | 0.79 | 88 | empty |
| 2 | 87 | 0.66 | 0.91 | 22 | empty |
| 3 | 65 | 0.66 | 0.93 | 21 | empty |
| 4 | 369 | 0.62 | 0.78 | 31 | empty |
| 5 | 281 | 0.53 | 0.75 | 28 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 710 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 707 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
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 P01031
- Elsewhere: RCSB PDB 5B4P · PDBe 5B4P · UniProt P01031
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