MolNFT v1 · #15166 · protein

Crystal structure of H365R mutant of 67 kda N-terminal fragment of E. COLI DNA topoisomerase I

1MW9: “Crystal structure of H365R mutant of 67 kda N-terminal fragment of E. COLI DNA topoisomerase I”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.65). MolNFT v1 #15166 on GenesisL1: 3D structure, binding sites and…

PDB: 1MW9
Type: protein
Length: 556 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA topoisomerase I
EC: 5.99.1.2
UniProt: P06612
Ligands: SO4
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	DNA topoisomerase I (EC 5.99.1.2)	protein	556	46% helix, 20% strand	P06612

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains X

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	80	0.65	0.91	15	empty
2	445	0.64	0.78	44	SO4
3	112	0.35	0.73	27	empty
4	69	0.33	0.76	15	empty
5	50	0.29	0.75	12	empty

Compared structures

1MW9 · Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA… · the same entry in another collection · chain X against X, TM-score 1.00
P06612 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P06612) · a predicted model of the same protein · chain X 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 P06612
Elsewhere: RCSB PDB 1MW9 · PDBe 1MW9 · UniProt P06612

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