MolNFT v1 · #55615 · protein

Kshv lana (ORF73) C-terminal domain, decameric ring: monoclinic crystal form

2YPY · Orf 73: “Kshv lana (ORF73) C-terminal domain, decameric ring: monoclinic crystal form”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.53). MolNFT v1 #55615 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2YPY
Type: protein
Length: 1,345 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Orf 73
UniProt: Q76SB0
Ligands: CL
Pockets: 20 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, H, I, J	Orf 73	protein	134	34% helix, 19% strand	Q76SB0
B, E	Orf 73	protein	136	33% helix, 21% strand	Q76SB0
C, D	Orf 73	protein	135	33% helix, 20% strand	Q76SB0
G	Orf 73	protein	133	31% helix, 20% strand	Q76SB0

Ligands and binding sites

CL · Chloride ion · ion · 24 copies · chains A, B, J, C, D, E, F, G, H, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	204	0.53	0.78	33	empty
2	185	0.51	0.78	27	empty
3	136	0.48	0.78	26	empty
4	245	0.47	0.73	38	CL
5	223	0.46	0.73	42	CL

Interfaces

10 interfaces between chains.

E–F · 2311 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2233 Å² buried · 15 hydrogen bonds · protein-protein
I–J · 2158 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2112 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 2095 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

2YPY · KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form · 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 Q76SB0
Elsewhere: RCSB PDB 2YPY · PDBe 2YPY · UniProt Q76SB0

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