MolNFT v1 · #138038 · protein

Crystal structure of bacteriophage CBA120 tailspike protein 2 enzymatically active domain (TSP2DN, ORF211)

5W6P: “Crystal structure of bacteriophage CBA120 tailspike protein 2 enzymatically active domain (TSP2DN, ORF211)”. X-ray diffraction, 2 ligands (ZN, K), 20 pockets (best druggability 0.87). MolNFT v1 #138038 on GenesisL1: 3D structure…

PDB: 5W6P
Type: protein
Length: 4,060 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tailspike protein 2
UniProt: G3M190
Ligands: ZN, K
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	Tailspike protein 2	protein	676	10% helix, 41% strand	G3M190
D	Tailspike protein 2	protein	677	10% helix, 42% strand	G3M190
F	Tailspike protein 2	protein	679	10% helix, 42% strand	G3M190

Ligands and binding sites

ZN · Zinc ion · metal · 40 copies · chains A, B, C, D, E, F
K · Potassium ion · metal · 2 copies · chains A, B, C, D, E, F
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, F, E

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	872	0.87	0.90	108	EDO, ZN
2	877	0.87	0.89	110	ZN
3	865	0.84	0.86	93	empty
4	826	0.84	0.86	83	empty
5	884	0.77	0.81	78	EDO

Interfaces

10 interfaces between chains.

A–C · 3462 Å² buried · 49 hydrogen bonds · protein-protein
D–E · 3435 Å² buried · 46 hydrogen bonds · protein-protein
B–C · 3429 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 3422 Å² buried · 44 hydrogen bonds · protein-protein
E–F · 3416 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

5W6P · Crystal structure of Bacteriophage CBA120 tailspike protein 2 enzymatically active domain… · 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 G3M190
Elsewhere: RCSB PDB 5W6P · PDBe 5W6P · UniProt G3M190

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