MolNFT v1 · #123605 · protein
Structure of the complex of human complement C4 with masp-2 rebuilt using imdff
5JPM · Complement C4-a: “Structure of the complex of human complement C4 with masp-2 rebuilt using imdff”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #123605 on GenesisL1: 3D structure, binding…
- PDB
- 5JPM
- Type
- protein
- Length
- 4,130 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C4-a; Mannan-binding lectin serine protease 2
- EC
- 3.4.21.104
- UniProt
- P0C0L4, O00187
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Complement C4-a | protein | 651 | 8% helix, 48% strand | P0C0L4 |
| B, E | Complement C4-a | protein | 740 | 35% helix, 24% strand | P0C0L4 |
| C, F | Complement C4-a | protein | 287 | 17% helix, 35% strand | P0C0L4 |
| G, I | Mannan-binding lectin serine protease 2 (EC 3.4.21.104) | protein | 145 | 0% helix, 35% strand | O00187 |
| H, J | Mannan-binding lectin serine protease 2 (EC 3.4.21.104) | protein | 242 | 10% helix, 35% strand | O00187 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, D, E
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.86 | 0.87 | 124 | empty |
| 2 | 1053 | 0.80 | 0.81 | 105 | empty |
| 3 | 93 | 0.75 | 0.96 | 26 | empty |
| 4 | 235 | 0.73 | 0.89 | 34 | empty |
| 5 | 856 | 0.73 | 0.78 | 61 | empty |
Interfaces
21 interfaces between chains.
- A–B · 4758 Ų buried · 77 hydrogen bonds · protein-protein
- D–E · 4758 Ų buried · 80 hydrogen bonds · protein-protein
- E–F · 4497 Ų buried · 64 hydrogen bonds · protein-protein
- B–C · 4495 Ų buried · 57 hydrogen bonds · protein-protein
- B–J · 1420 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 6 glycan, 4 modified (disulfide, N-glycosylation, sulfation).
Compared structures
- 5JPM · Structure of the complex of human complement C4 with MASP-2 rebuilt using iMDFF · the same entry in another collection · chain J against J, TM-score 1.00
- O00187 · AlphaFold monomer V2.0 prediction for mannan-binding lectin serine protease 2 (O00187) · a predicted model of the same protein · chain H against A, TM-score 0.97
- P0C0L4 · AlphaFold monomer V2.0 prediction for complement C4-a (P0C0L4) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0C0L4
- Every structure of UniProt O00187
- Elsewhere: RCSB PDB 5JPM · PDBe 5JPM · UniProt P0C0L4 · UniProt O00187
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