MolNFT v1 · #118804 · protein + DNA

Structure of LIN54 tesmin domain bound to DNA

5FD3 · Protein lin-54 homolog: “Structure of LIN54 tesmin domain bound to DNA”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.66). MolNFT v1 #118804 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FD3
Type: protein + DNA
Length: 264 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein lin-54 homolog; DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3'); DNA…
UniProt: Q6MZP7
Ligands: ZN
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein lin-54 homolog	protein	108	30% helix, 0% strand	Q6MZP7
B	Protein lin-54 homolog	protein	108	30% helix, 0% strand	Q6MZP7
C, H	DNA (5'-D(GPAPGPTPTPTPGPAPAPAPCPT)-3')	dna	12	—	—
D, I	DNA (5'-D(CPAPGPTPTPTPCPAPAPAPCPTP*C)-3')	dna	12	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B

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

Pockets

5 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	387	0.66	0.80	45	empty
2	266	0.65	0.82	32	empty
3	92	0.41	0.78	20	empty
4	63	0.26	0.72	13	empty
5	54	0.25	0.73	13	empty

Interfaces

7 interfaces between chains.

A–H · 595 Å² buried · 17 hydrogen bonds · protein-nucleic
B–C · 595 Å² buried · 13 hydrogen bonds · protein-nucleic
B–D · 537 Å² buried · 13 hydrogen bonds · protein-nucleic
C–D · 513 Å² buried · 56 hydrogen bonds · nucleic-nucleic
H–I · 512 Å² buried · 53 hydrogen bonds · nucleic-nucleic

Compared structures

5FD3 · Structure of Lin54 tesmin domain bound to DNA · the same entry in another collection · chain I against I, TM-score 1.00
Q6MZP7 · AlphaFold monomer V2.0 prediction for protein lin-54 homolog (Q6MZP7) · a predicted model of the same protein · chain B 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 Q6MZP7
Elsewhere: RCSB PDB 5FD3 · PDBe 5FD3 · UniProt Q6MZP7

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