MolNFT v1 · #15842 · protein + DNA

Human topoisomerase I ara-C complex

1NH3 · 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3': “Human topoisomerase I ara-C complex”. X-ray diffraction, 6 pockets (best druggability 0.86). MolNFT v1 #15842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NH3
Type: protein + DNA
Length: 515 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3'; 5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)…
EC: 5.99.1.2
UniProt: P11387
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-D(APAPAPAPAPGPAPCPUP(UBB))-3'	dna	10	—	—
C	5'-D((GNG)PGPAPAPAPAPAPUPUPUPUPT)-3'	dna	12	—	—
D	5'-D(APAPAPAPAPTPUPUPUPUPCP(CAR) PAPAPGPUPCPUPUPUPUPT)-3'	dna	22	—	—
A	DNA topoisomerase I (EC 5.99.1.2)	protein	471	34% helix, 13% strand	P11387

Pockets

6 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	930	0.86	0.88	92	empty
2	714	0.73	0.80	57	empty
3	100	0.49	0.81	20	empty
4	66	0.48	0.84	21	empty
5	53	0.42	0.83	16	empty

Interfaces

6 interfaces between chains.

D–A · 837 Å² buried · 21 hydrogen bonds · protein-nucleic
B–A · 564 Å² buried · 15 hydrogen bonds · protein-nucleic
C–D · 526 Å² buried · 37 hydrogen bonds · nucleic-nucleic
B–D · 431 Å² buried · 34 hydrogen bonds · nucleic-nucleic
C–A · 248 Å² buried · 5 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification, phosphorylation).

Compared structures

1NH3 · Human Topoisomerase I Ara-C Complex · the same entry in another collection · chain B against B, TM-score 1.00
P11387 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P11387) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P11387
Elsewhere: RCSB PDB 1NH3 · PDBe 1NH3 · UniProt P11387

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