MolNFT v1 · #191151 · protein + DNA

Trai trans-esterase domain from PKM101 (DNA bound)

8A1C: “Trai trans-esterase domain from PKM101 (DNA bound)”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.68). MolNFT v1 #191151 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8A1C
Type: protein + DNA
Length: 311 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Trai; 11MER orit DNA
UniProt: D9Z5Q2
Ligands: MN
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Trai	protein	301	40% helix, 21% strand	D9Z5Q2
C	11MER orit DNA	dna	10	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · chains A, C

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	432	0.68	0.81	35	empty
2	149	0.55	0.81	24	empty
3	127	0.43	0.77	21	MN
4	74	0.40	0.79	23	empty
5	104	0.38	0.76	19	empty

Interfaces

1 interface between chains.

A–C · 1467 Å² buried · 42 hydrogen bonds · protein-nucleic

Compared structures

8A1C · TraI trans-esterase domain from pKM101 (DNA bound) · the same entry in another collection · chain A against A, 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 D9Z5Q2
Elsewhere: RCSB PDB 8A1C · PDBe 8A1C · UniProt D9Z5Q2

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