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Crystal structure from a single-stranded DNA binding protein from the lactococcal phage P2

Analyse Crystal structure from a single-stranded DNA binding protein from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WKC
Type: protein
Length: 358 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ORF34P2
UniProt: Q09WL7
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 60% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	ORF34P2	protein	90	0% helix, 60% strand	Q09WL7
B	ORF34P2	protein	89	0% helix, 64% strand	Q09WL7
D	ORF34P2	protein	89	0% helix, 56% strand	Q09WL7

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	259	0.51	0.75	26	empty
2	184	0.45	0.74	22	empty
3	131	0.40	0.74	21	empty
4	134	0.40	0.74	21	empty
5	77	0.33	0.74	16	empty

Interfaces

6 interfaces between chains.

C–D · 1170 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1150 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 535 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 491 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 483 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2WKC · Crystal structure from a single-stranded DNA binding protein from the lactococcal phage p2 · the same entry in another collection · chain A against A, 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 Q09WL7
Elsewhere: RCSB PDB 2WKC · PDBe 2WKC · UniProt Q09WL7

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