MolNFT v1 · #182463 · protein + RNA

Structure of HIV-1 matrix domain bound to human TRNALYS3

7MRL: “Structure of HIV-1 matrix domain bound to human TRNALYS3”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.78). MolNFT v1 #182463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7MRL
Type: protein + RNA
Length: 278 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 matrix domain; TRNA LYS3
UniProt: C1JB69
Ligands: MG
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	HIV-1 matrix domain	protein	102	69% helix, 3% strand	C1JB69
A	TRNA LYS3	rna	75	—	—
B	HIV-1 matrix domain	protein	101	65% helix, 3% strand	C1JB69

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

4 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	543	0.78	0.85	50	MG
2	1087	0.75	0.78	55	empty
3	194	0.47	0.76	16	empty
4	61	0.29	0.75	10	empty

Interfaces

2 interfaces between chains.

C–A · 880 Å² buried · 14 hydrogen bonds · protein-nucleic
A–B · 568 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

7MRL · Structure of HIV-1 matrix domain bound to human tRNALys3 · the same entry in another collection · chain C against C, 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 C1JB69
Elsewhere: RCSB PDB 7MRL · PDBe 7MRL · UniProt C1JB69

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