MolNFT v1 · #76630 · protein
Crystal structure of non-symbiotic plant hemoglobin from trema tomentosa
3QQQ · Non-symbiotic hemoglobin: “Crystal structure of non-symbiotic plant hemoglobin from trema tomentosa”. X-ray diffraction, 2 ligands (HEM, SO4), 4 pockets (best druggability 0.70). MolNFT v1 #76630 on GenesisL1: 3D structure, binding…
- PDB
- 3QQQ
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-symbiotic hemoglobin
- UniProt
- P07803
- Ligands
- HEM, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-symbiotic hemoglobin | protein | 150 | 77% helix, 0% strand | P07803 |
| B | Non-symbiotic hemoglobin | protein | 149 | 78% helix, 0% strand | P07803 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.70 | 0.85 | 35 | HEM |
| 2 | 226 | 0.70 | 0.85 | 32 | HEM |
| 3 | 90 | 0.37 | 0.75 | 19 | SO4 |
| 4 | 74 | 0.36 | 0.77 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3QQQ · Crystal structure of non-symbiotic plant hemoglobin from Trema tomentosa · the same entry in another collection · chain B against B, TM-score 1.00
- P07803 · AlphaFold monomer V2.0 prediction for non-symbiotic hemoglobin (P07803) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P07803
- Elsewhere: RCSB PDB 3QQQ · PDBe 3QQQ · UniProt P07803
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