MolNFT v1 · #176011 · protein

Mitf bhlhlz apo structure

7D8S · Microphthalmia-associated transcription FACTOR,METHIONYL…: “Mitf bhlhlz apo structure”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.65). MolNFT v1 #176011 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7D8S
Type: protein
Length: 724 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microphthalmia-associated transcription FACTOR,METHIONYL- tRNA synthetase beta subunit
UniProt: O75030, O66738
Ligands: SO4
Pockets: 10 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microphthalmia-associated transcription FACTOR,METHIONYL- tRNA synthetase beta subunit	protein	185	32% helix, 26% strand	O75030, O66738
B	Microphthalmia-associated transcription FACTOR,METHIONYL- tRNA synthetase beta subunit	protein	180	33% helix, 27% strand	O75030, O66738
C	Microphthalmia-associated transcription FACTOR,METHIONYL- tRNA synthetase beta subunit	protein	184	33% helix, 27% strand	O75030, O66738
D	Microphthalmia-associated transcription FACTOR,METHIONYL- tRNA synthetase beta subunit	protein	175	35% helix, 27% strand	O75030, O66738

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	316	0.65	0.81	46	SO4
2	291	0.61	0.79	41	SO4
3	109	0.46	0.79	20	empty
4	126	0.43	0.76	19	empty
5	59	0.39	0.80	19	empty

Interfaces

6 interfaces between chains.

B–C · 2750 Å² buried · 42 hydrogen bonds · protein-protein
A–D · 2732 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 1504 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1449 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 517 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7D8S · MITF bHLHLZ apo structure · the same entry in another collection · chain D against D, TM-score 1.00
O75030 · AlphaFold monomer V2.0 prediction for microphthalmia-associated transcription factor… · a predicted model of the same protein · chain C against A, TM-score 0.39

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 O75030
Every structure of UniProt O66738
Elsewhere: RCSB PDB 7D8S · PDBe 7D8S · UniProt O75030 · UniProt O66738

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