MolNFT v1 · #17884 · protein + DNA

Anabaena hu-DNA corcrystal structure (TR3)

1P71 · 5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP…: “Anabaena hu-DNA corcrystal structure (TR3)”. X-ray diffraction, 2 pockets (best druggability 0.77). MolNFT v1 #17884 on GenesisL1: 3D structure, binding sites and…

PDB: 1P71
Type: protein + DNA
Length: 226 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP *AP*CP*C)-3'; DNA-binding…
UniProt: P05514
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	5'-D(TPGPCPTPTPAPTPCPAPAPTPTPTPGPTPTPGPCP APCP*C)-3'	dna	19	—	—
D	5'-D(TPGPCPTPTPAPTPCPAPAPTPTPTPGPTPTPGPCP APCP*C)-3'	dna	20	—	—
A	DNA-binding protein hu	protein	94	41% helix, 30% strand	P05514
B	DNA-binding protein hu	protein	93	42% helix, 30% strand	P05514

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	900	0.77	0.80	78	empty
2	97	0.30	0.71	12	empty

Interfaces

6 interfaces between chains.

A–B · 2001 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 859 Å² buried · 84 hydrogen bonds · nucleic-nucleic
D–B · 527 Å² buried · 5 hydrogen bonds · protein-nucleic
C–A · 511 Å² buried · 7 hydrogen bonds · protein-nucleic
D–A · 358 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

1P71 · Anabaena HU-DNA corcrystal structure (TR3) · the same entry in another collection · chain C against C, TM-score 1.00
P05514 · AlphaFold monomer V2.0 prediction for DNA-binding protein hu (P05514) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 P05514
Elsewhere: RCSB PDB 1P71 · PDBe 1P71 · UniProt P05514

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