MolNFT v1 · #17795 · protein

F factor trai relaxase domain

1P4D · Trai protein: “F factor trai relaxase domain”. X-ray diffraction, 1 ligand (MG), 13 pockets (best druggability 0.77). MolNFT v1 #17795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1P4D
Type: protein
Length: 827 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trai protein
EC: 3.6.1.-
UniProt: P14565
Ligands: MG
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trai protein (EC 3.6.1.-)	protein	275	40% helix, 22% strand	P14565
B, C	Trai protein (EC 3.6.1.-)	protein	276	40% helix, 21% strand	P14565

Ligands and binding sites

MG · Magnesium ion · metal · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C

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

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	882	0.77	0.80	77	EDO
2	498	0.63	0.76	52	empty
3	239	0.51	0.76	30	empty
4	194	0.49	0.76	26	empty
5	204	0.47	0.75	37	MG

Interfaces

2 interfaces between chains.

A–B · 956 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 790 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1P4D · F factor TraI Relaxase Domain · the same entry in another collection · chain A against A, TM-score 1.00
P14565 · AlphaFold monomer V2.0 prediction for multifunctional conjugation protein trai (P14565) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P14565
Elsewhere: RCSB PDB 1P4D · PDBe 1P4D · UniProt P14565

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