MolNFT v1 · #102654 · protein

Dimer of a C-terminal fragment of phage T4 GP5 beta-helix

4OSD · Tail-associated lysozyme: “Dimer of a C-terminal fragment of phage T4 GP5 beta-helix”. X-ray diffraction, 4 ligands (ELA, STE, PLM), 10 pockets (best druggability 0.85). MolNFT v1 #102654 on GenesisL1: 3D structure, binding sites…

PDB: 4OSD
Type: protein
Length: 1,672 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tail-associated lysozyme
EC: 3.2.1.17
UniProt: P16009
Ligands: ELA, STE, PLM, MG
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 66% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, J, K, M, N, O, P, Q, R	Tail-associated lysozyme (EC 3.2.1.17)	protein	93	0% helix, 66% strand	P16009
I, L	Tail-associated lysozyme (EC 3.2.1.17)	protein	92	0% helix, 66% strand	P16009

Ligands and binding sites

ELA · 9-octadecenoic acid · ligand · 7 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
STE · Stearic acid · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
PLM · Palmitic acid · ligand · 5 copies · chains D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R

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

Pockets

10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.85	0.85	74	ELA, STE, PLM
2	1127	0.84	0.85	75	ELA, STE
3	1199	0.84	0.85	74	STE, ELA, PLM
4	1150	0.84	0.85	74	PLM, STE, ELA
5	1160	0.84	0.85	76	STE, ELA, PLM

Interfaces

68 interfaces between chains.

B–C · 3743 Å² buried · 106 hydrogen bonds · protein-protein
A–C · 3739 Å² buried · 111 hydrogen bonds · protein-protein
D–F · 3735 Å² buried · 106 hydrogen bonds · protein-protein
M–N · 3726 Å² buried · 112 hydrogen bonds · protein-protein
E–F · 3721 Å² buried · 106 hydrogen bonds · protein-protein

Compared structures

4OSD · Dimer of a C-terminal fragment of phage T4 gp5 beta-helix · 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 P16009
Elsewhere: RCSB PDB 4OSD · PDBe 4OSD · UniProt P16009

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