MolNFT v1 · #101647 · protein

Crystal structure of the cytosolic domain of human MID51

4NXU · Mitochondrial dynamic protein MID51: “Crystal structure of the cytosolic domain of human MID51”. X-ray diffraction, 2 ligands (ADP, SO4), 14 pockets (best druggability 0.80). MolNFT v1 #101647 on GenesisL1: 3D structure, binding…

PDB: 4NXU
Type: protein
Length: 1,313 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial dynamic protein MID51
UniProt: Q9NQG6
Ligands: ADP, SO4
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitochondrial dynamic protein MID51	protein	327	50% helix, 17% strand	Q9NQG6
B	Mitochondrial dynamic protein MID51	protein	328	49% helix, 18% strand	Q9NQG6
C	Mitochondrial dynamic protein MID51	protein	332	48% helix, 17% strand	Q9NQG6
D	Mitochondrial dynamic protein MID51	protein	326	48% helix, 18% strand	Q9NQG6

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, C
GOL · Glycerol · additive · 2 copies · chains B, C

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	895	0.80	0.83	115	ADP
2	638	0.77	0.82	48	empty
3	571	0.74	0.81	65	ADP
4	418	0.73	0.83	40	empty
5	625	0.71	0.79	53	ADP

Interfaces

5 interfaces between chains.

B–D · 602 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 549 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 440 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 236 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 118 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4NXU · Crystal structure of the cytosolic domain of human MiD51 · the same entry in another collection · chain D against D, TM-score 1.00
Q9NQG6 · AlphaFold monomer V2.0 prediction for mitochondrial dynamics protein MID51 (Q9NQG6) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 Q9NQG6
Elsewhere: RCSB PDB 4NXU · PDBe 4NXU · UniProt Q9NQG6

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