MolNFT v1 · #156290 · protein
Crystal structure of pmab-1 fv-clasp fragment with its antigen peptide
6LZ4 · Pmab-1 VH(S112C)-sarah chimera: “Crystal structure of pmab-1 fv-clasp fragment with its antigen peptide”. X-ray diffraction, 11 pockets (best druggability 0.64). MolNFT v1 #156290 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6LZ4
- Type
- protein
- Length
- 653 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pmab-1 VH(S112C)-sarah chimera; Pmab-1 vl-SARAH(S37C) chimera; MAP peptide
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pmab-1 VH(S112C)-sarah chimera | protein | 163 | 30% helix, 37% strand | — |
| B | Pmab-1 vl-SARAH(S37C) chimera | protein | 162 | 28% helix, 34% strand | — |
| C | MAP peptide | protein | 8 | 0% helix, 0% strand | — |
| D | Pmab-1 VH(S112C)-sarah chimera | protein | 163 | 28% helix, 39% strand | — |
| E | Pmab-1 vl-SARAH(S37C) chimera | protein | 150 | 28% helix, 36% strand | — |
| F | MAP peptide | protein | 7 | 0% helix, 0% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.64 | 0.78 | 44 | empty |
| 2 | 403 | 0.58 | 0.75 | 40 | empty |
| 3 | 84 | 0.55 | 0.85 | 14 | empty |
| 4 | 218 | 0.50 | 0.76 | 24 | empty |
| 5 | 172 | 0.43 | 0.74 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2460 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2273 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 349 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 305 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6LZ4 · Crystal structure of PMab-1 Fv-clasp fragment with its antigen peptide · 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 6LZ4 · PDBe 6LZ4
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