MolNFT v1 · #157564 · protein

Microed structure of the ctd-SP1 fragment of HIV-1 gag

6N3J: “Microed structure of the ctd-SP1 fragment of HIV-1 gag”. Electron crystallography, 4 pockets (best druggability 0.76). MolNFT v1 #157564 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N3J
Type: protein
Length: 545 residues
Chains: 6
Method: electron crystallography
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ctd-SP1 fragment of HIV-1 gag
UniProt: A0A248SMC7
Pockets: 4 · best druggability 0.76

Structure

electron crystallography · 2 distinct chains · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F	Ctd-SP1 fragment of HIV-1 gag	protein	91	66% helix, 0% strand	A0A248SMC7
D	Ctd-SP1 fragment of HIV-1 gag	protein	90	68% helix, 0% strand	A0A248SMC7

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	987	0.76	0.78	108	empty
2	119	0.50	0.80	29	empty
3	55	0.31	0.76	21	empty
4	54	0.29	0.75	18	empty

Interfaces

6 interfaces between chains.

A–F · 696 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 678 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 676 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 661 Å² buried · 4 hydrogen bonds · protein-protein
D–E · 647 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6N3J · MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag · the same entry in another collection · chain B against B, 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 A0A248SMC7
Elsewhere: RCSB PDB 6N3J · PDBe 6N3J · UniProt A0A248SMC7

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