MolNFT v1 · #110101 · protein
Crystal structure of nitrophorin 7 from rhodnius prolixus at pH 7.8 complexed with gly-gly-gly
4XMH · Nitrophorin-7: “Crystal structure of nitrophorin 7 from rhodnius prolixus at pH 7.8 complexed with gly-gly-gly”. X-ray diffraction, 1 ligand (HEM), 1 pocket (best druggability 0.67). MolNFT v1 #110101 on GenesisL1: 3D structure…
- PDB
- 4XMH
- Type
- protein
- Length
- 188 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrophorin-7; Gly-gly-gly
- EC
- 1.7.6.1
- UniProt
- Q6PQK2
- Ligands
- HEM
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrophorin-7 (EC 1.7.6.1) | protein | 185 | 11% helix, 46% strand | Q6PQK2 |
| B | Gly-gly-gly | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.67 | 0.82 | 35 | HEM |
Interfaces
1 interface between chains.
- A–B · 204 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4XMH · Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6PQK2 · AlphaFold monomer V2.0 prediction for nitrophorin-7 (Q6PQK2) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6PQK2
- Elsewhere: RCSB PDB 4XMH · PDBe 4XMH · UniProt Q6PQK2
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