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Crystal structure of a DNA2 peptide in complex with rpa 70N

Analyse Crystal structure of a DNA2 peptide in complex with rpa 70N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EAY
Type: protein
Length: 502 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replication protein a 70 kda DNA-binding subunit; DNA replication ATP-dependent…
UniProt: P27694, P51530
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Replication protein a 70 kda DNA-binding subunit	protein	115	17% helix, 43% strand	P27694
C	Replication protein a 70 kda DNA-binding subunit	protein	112	17% helix, 45% strand	P27694
D	Replication protein a 70 kda DNA-binding subunit	protein	112	18% helix, 45% strand	P27694
E	DNA replication ATP-dependent HELICASE/NUCLEASE DNA2	protein	12	33% helix, 0% strand	P51530
F, G, H	DNA replication ATP-dependent HELICASE/NUCLEASE DNA2	protein	12	33% helix, 0% strand	P51530

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	604	0.65	0.76	47	empty
2	338	0.61	0.78	32	empty
3	401	0.61	0.76	34	empty
4	273	0.61	0.80	30	empty
5	386	0.60	0.76	30	empty

Interfaces

11 interfaces between chains.

B–G · 684 Å² buried · 6 hydrogen bonds · protein-protein
A–H · 673 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 648 Å² buried · 7 hydrogen bonds · protein-protein
C–F · 629 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 532 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5EAY · Crystal structure of a Dna2 peptide in complex with Rpa 70N · the same entry in another collection · chain H against H, TM-score 1.00
P27694 · AlphaFold monomer V2.0 prediction for replication protein a 70 kda DNA-binding subunit… · a predicted model of the same protein · chain D against A, TM-score 0.98
P51530 · AlphaFold monomer V2.0 prediction for DNA replication ATP-dependent HELICASE/NUCLEASE… · a predicted model of the same protein · chain H against A, TM-score 0.58

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 P27694
Every structure of UniProt P51530
Elsewhere: RCSB PDB 5EAY · PDBe 5EAY · UniProt P27694 · UniProt P51530

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