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Hbb-DNA complex

Analyse Hbb-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NP2
Type: protein + DNA
Length: 274 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 36-mer; Hbb
UniProt: Q3I4Z2
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	36-mer	dna	35	—	—
A, B	Hbb	protein	102	41% helix, 26% strand	Q3I4Z2

Pockets

5 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	1139	0.85	0.86	93	empty
2	182	0.47	0.76	25	empty
3	131	0.39	0.74	22	empty
4	99	0.38	0.76	16	empty
5	115	0.38	0.75	18	empty

Interfaces

6 interfaces between chains.

A–B · 2761 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1488 Å² buried · 143 hydrogen bonds · nucleic-nucleic
D–B · 816 Å² buried · 21 hydrogen bonds · protein-nucleic
C–A · 785 Å² buried · 21 hydrogen bonds · protein-nucleic
D–A · 757 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

2NP2 · Hbb-DNA complex · the same entry in another collection · chain C against C, 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 Q3I4Z2
Elsewhere: RCSB PDB 2NP2 · PDBe 2NP2 · UniProt Q3I4Z2

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