MolNFT v1 · #170132 · protein
Crystal structure of NB7, a nanobody targeting prostate specific membrane antigen
6XXN · NB_7_A,B,C,F: “Crystal structure of NB7, a nanobody targeting prostate specific membrane antigen”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.84). MolNFT v1 #170132 on GenesisL1: 3D structure, binding sites…
- PDB
- 6XXN
- Type
- protein
- Length
- 996 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NB_7_A,B,C,F; NB_7_G; NB_7_H
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | NB_7_A,B,C,F | protein | 125 | 2% helix, 48% strand | — |
| D, E | NB_7_A,B,C,F | protein | 124 | 5% helix, 48% strand | — |
| G | NB_7_G | protein | 124 | 7% helix, 48% strand | — |
| H | NB_7_H | protein | 124 | 5% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, H, E, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.84 | 0.86 | 124 | empty |
| 2 | 1169 | 0.83 | 0.84 | 112 | empty |
| 3 | 196 | 0.47 | 0.75 | 29 | SO4 |
| 4 | 134 | 0.45 | 0.77 | 27 | empty |
| 5 | 130 | 0.44 | 0.77 | 24 | empty |
Interfaces
13 interfaces between chains.
- C–F · 746 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 732 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 703 Ų buried · 17 hydrogen bonds · protein-protein
- D–G · 644 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 485 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6XXN · Crystal structure of NB7, a nanobody targeting prostate specific membrane antigen · 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 6XXN · PDBe 6XXN
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