MolNFT v1 · #141544 · protein

Dimeric crystal structure of ORF57 from kshv

5ZB3: “Dimeric crystal structure of ORF57 from kshv”. X-ray diffraction, 1 ligand (ZN), 17 pockets (best druggability 0.73). MolNFT v1 #141544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZB3
Type: protein
Length: 560 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ORF57
UniProt: A0A0N9SHG8
Ligands: ZN
Pockets: 17 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ORF57	protein	280	56% helix, 1% strand	A0A0N9SHG8

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 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	623	0.73	0.80	59	empty
2	459	0.68	0.79	58	empty
3	131	0.54	0.82	25	empty
4	142	0.53	0.80	21	empty
5	97	0.51	0.82	15	empty

Interfaces

1 interface between chains.

A–B · 3739 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

5ZB3 · Dimeric crystal structure of ORF57 from KSHV · 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 A0A0N9SHG8
Elsewhere: RCSB PDB 5ZB3 · PDBe 5ZB3 · UniProt A0A0N9SHG8

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