MolNFT v1 · #114235 · protein
Crystal structure of the Fab fragment of an anti-leukotriene C4 monoclonal antibody complexed with LTC4
5B6F · Anti-leukotriene C4 monoclonal antibody immunoglobulin…: “Crystal structure of the Fab fragment of an anti-leukotriene C4 monoclonal antibody complexed with LTC4”. X-ray diffraction, 2 ligands (LTX, SO4), 19 pockets (best…
- PDB
- 5B6F
- Type
- protein
- Length
- 1,710 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain…
- Ligands
- LTX, SO4
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain | protein | 216 | 6% helix, 52% strand | — |
| B | Anti-leukotriene C4 monoclonal antibody immunoglobulin GAMMA1 heavy chain | protein | 211 | 10% helix, 52% strand | — |
| C, G | Anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain | protein | 217 | 6% helix, 53% strand | — |
| D | Anti-leukotriene C4 monoclonal antibody immunoglobulin GAMMA1 heavy chain | protein | 211 | 9% helix, 54% strand | — |
| F | Anti-leukotriene C4 monoclonal antibody immunoglobulin GAMMA1 heavy chain | protein | 212 | 10% helix, 53% strand | — |
| H | Anti-leukotriene C4 monoclonal antibody immunoglobulin GAMMA1 heavy chain | protein | 210 | 7% helix, 52% strand | — |
Ligands and binding sites
- LTX · (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-(2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11, 14-tetraenoic acid · ligand · 4 copies · chains A, B, H, C, D, E, F, G
- SO4 · Sulfate ion · ion · 6 copies · chains B, G, C, F, D, E, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.79 | 0.80 | 107 | SO4 |
| 2 | 1106 | 0.78 | 0.80 | 95 | SO4 |
| 3 | 126 | 0.75 | 0.93 | 23 | LTX |
| 4 | 129 | 0.74 | 0.93 | 23 | empty |
| 5 | 137 | 0.72 | 0.91 | 24 | LTX |
Interfaces
13 interfaces between chains.
- E–F · 1699 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1684 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1640 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1619 Ų buried · 17 hydrogen bonds · protein-protein
- B–G · 450 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5B6F · Crystal structure of the Fab fragment of an anti-Leukotriene C4 monoclonal antibody… · 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
- Elsewhere: RCSB PDB 5B6F · PDBe 5B6F
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