MolNFT v1 · #139341 · protein
Crystal structure of nz-1 fv-clasp fragment with its antigen peptide
5XCV · VH(S112C)-sarah CHIMERA,VH(S112C)-sarah chimera: “Crystal structure of nz-1 fv-clasp fragment with its antigen peptide”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.87). MolNFT v1 #139341 on GenesisL1: 3D…
- PDB
- 5XCV
- Type
- protein
- Length
- 665 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VH(S112C)-sarah CHIMERA,VH(S112C)-sarah chimera; Vl-SARAH(S37C) CHIMERA,VL-SARAH(S37C)…
- Ligands
- CA
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VH(S112C)-sarah CHIMERA,VH(S112C)-sarah chimera | protein | 169 | 32% helix, 37% strand | — |
| B | Vl-SARAH(S37C) CHIMERA,VL-SARAH(S37C) chimera | protein | 149 | 32% helix, 33% strand | — |
| C | PA14 peptide | protein | 11 | 0% helix, 0% strand | — |
| D | VH(S112C)-sarah CHIMERA,VH(S112C)-sarah chimera | protein | 167 | 32% helix, 39% strand | — |
| E | Vl-SARAH(S37C) CHIMERA,VL-SARAH(S37C) chimera | protein | 160 | 31% helix, 33% strand | — |
| F | PA14 peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.87 | 0.88 | 125 | empty |
| 2 | 202 | 0.47 | 0.74 | 26 | empty |
| 3 | 63 | 0.32 | 0.76 | 16 | empty |
| 4 | 73 | 0.31 | 0.74 | 23 | empty |
Interfaces
10 interfaces between chains.
- D–E · 2458 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2209 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1198 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 536 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5XCV · Crystal structure of NZ-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 5XCV · PDBe 5XCV
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