MolNFT v1 · #49986 · protein

The crystal structure of nonsymbiotic corn hemoglobin 1

2R50 · Non-symbiotic hemoglobin: “The crystal structure of nonsymbiotic corn hemoglobin 1”. X-ray diffraction, 2 ligands (HEM, SO4), 11 pockets (best druggability 0.74). MolNFT v1 #49986 on GenesisL1: 3D structure, binding sites and…

PDB: 2R50
Type: protein
Length: 584 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-symbiotic hemoglobin
UniProt: Q9M593
Ligands: HEM, SO4
Pockets: 11 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Non-symbiotic hemoglobin	protein	146	74% helix, 0% strand	Q9M593
B	Non-symbiotic hemoglobin	protein	146	78% helix, 0% strand	Q9M593
C	Non-symbiotic hemoglobin	protein	147	77% helix, 0% strand	Q9M593
D	Non-symbiotic hemoglobin	protein	145	80% helix, 0% strand	Q9M593

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains B, C, A, D
ACY · Acetic acid · additive · 2 copies · chains B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.74	0.86	42	HEM, ACY
2	325	0.74	0.85	41	HEM, ACY
3	310	0.71	0.84	31	HEM
4	285	0.71	0.84	29	HEM
5	151	0.46	0.76	22	empty

Interfaces

4 interfaces between chains.

C–D · 516 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 510 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 361 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 332 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2R50 · The crystal structure of nonsymbiotic corn hemoglobin 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9M593 · AlphaFold monomer V2.0 prediction for non-symbiotic hemoglobin (Q9M593) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q9M593
Elsewhere: RCSB PDB 2R50 · PDBe 2R50 · UniProt Q9M593

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