MolNFT v1 · #125216 · protein
Crystal structure of W26A mutant of anti-EGFR centyrin P54AR4-83V2
5L2H: “Crystal structure of W26A mutant of anti-EGFR centyrin P54AR4-83V2”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #125216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L2H
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Centyrin
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Centyrin | protein | 97 | 0% helix, 55% strand | — |
| B | Centyrin | protein | 98 | 0% helix, 57% strand | — |
| D | Centyrin | protein | 96 | 0% helix, 58% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.68 | 0.81 | 68 | GOL |
| 2 | 165 | 0.48 | 0.77 | 41 | GOL |
| 3 | 62 | 0.37 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 332 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 331 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 312 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5L2H · Crystal Structure of W26A mutant of anti-EGFR Centyrin P54AR4-83v2 · 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 5L2H · PDBe 5L2H
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