MolNFT v1 · #124056 · protein

Rhesus macaques TRIM5ALPHA BBOX2 domain

5K3Q · Tripartite motif-containing protein 5,TRIPARTITE motif…: “Rhesus macaques TRIM5ALPHA BBOX2 domain”. X-ray diffraction, 2 ligands (ZN, NO3), 1 pocket (best druggability 0.53). MolNFT v1 #124056 on GenesisL1: 3D structure, binding…

PDB: 5K3Q
Type: protein
Length: 169 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tripartite motif-containing protein 5,TRIPARTITE motif- containing protein 5
EC: 6.3.2.-
UniProt: Q0PF16
Ligands: ZN, NO3
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tripartite motif-containing protein 5,TRIPARTITE motif- containing protein 5 (EC 6.3.2.-)	protein	43	19% helix, 26% strand	Q0PF16
B	Tripartite motif-containing protein 5,TRIPARTITE motif- containing protein 5 (EC 6.3.2.-)	protein	43	19% helix, 26% strand	Q0PF16
C	Tripartite motif-containing protein 5,TRIPARTITE motif- containing protein 5 (EC 6.3.2.-)	protein	42	17% helix, 26% strand	Q0PF16
D	Tripartite motif-containing protein 5,TRIPARTITE motif- containing protein 5 (EC 6.3.2.-)	protein	41	20% helix, 27% strand	Q0PF16

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
NO3 · Nitrate ion · ion · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	289	0.53	0.75	37	empty

Interfaces

4 interfaces between chains.

C–D · 482 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 465 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 246 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 80 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5K3Q · Rhesus macaques Trim5alpha Bbox2 domain · the same entry in another collection · chain D against D, TM-score 1.00
Q0PF16 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 5 (Q0PF16) · a predicted model of the same protein · chain C against A, TM-score 0.91

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 Q0PF16
Elsewhere: RCSB PDB 5K3Q · PDBe 5K3Q · UniProt Q0PF16

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.