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The ni-bound dimeric structure of K78H/G80A/H82A myoglobin

Analyse The ni-bound dimeric structure of K78H/G80A/H82A myoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DGL
Type: protein
Length: 306 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myoglobin
UniProt: P68082
Ligands: HEM, NI, O
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 82% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Myoglobin	protein	153	82% helix, 0% strand	P68082

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 2 copies · chains A, B
O · Oxygen atom · ion · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	228	0.71	0.86	30	HEM, O
2	217	0.71	0.86	29	O, HEM
3	372	0.66	0.80	41	empty

Interfaces

1 interface between chains.

A–B · 2886 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

7DGL · The Ni-bound dimeric structure of K78H/G80A/H82A myoglobin · 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
Every structure of UniProt P68082
Elsewhere: RCSB PDB 7DGL · PDBe 7DGL · UniProt P68082

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