MolNFT v1 · #37821 · protein

Leghemoglobin (oxy)

2GDM: “Leghemoglobin (oxy)”. X-ray diffraction, 2 ligands (HEM, OXY), 1 pocket (best druggability 0.72). MolNFT v1 #37821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GDM
Type: protein
Length: 153 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leghemoglobin (oxy)
UniProt: P02240
Ligands: HEM, OXY
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Leghemoglobin (oxy)	protein	153	77% helix, 0% strand	P02240

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
OXY · Oxygen molecule · ion · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.72	0.85	28	HEM, OXY

Compared structures

2GDM · Leghemoglobin (oxy) · the same entry in another collection · chain A against A, TM-score 1.00
P02240 · AlphaFold monomer V2.0 prediction for leghemoglobin-2 (P02240) · 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 P02240
Elsewhere: RCSB PDB 2GDM · PDBe 2GDM · UniProt P02240

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