MolNFT v1 · #117579 · protein

Ligand binding domain 1 of penicillium marneffei MP1 protein complexed with arachidonic acids

5ECF · Cell wall antigen: “Ligand binding domain 1 of penicillium marneffei MP1 protein complexed with arachidonic acids”. X-ray diffraction, 1 ligand (ACD), 20 pockets (best druggability 0.86). MolNFT v1 #117579 on GenesisL1: 3D…

PDB: 5ECF
Type: protein
Length: 1,476 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell wall antigen
UniProt: A0A093VKV7
Ligands: ACD
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 84% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cell wall antigen	protein	151	83% helix, 0% strand	A0A093VKV7
B	Cell wall antigen	protein	150	83% helix, 0% strand	A0A093VKV7
C, D, H, I	Cell wall antigen	protein	149	83% helix, 0% strand	A0A093VKV7
E, G	Cell wall antigen	protein	150	83% helix, 0% strand	A0A093VKV7
F	Cell wall antigen	protein	146	84% helix, 0% strand	A0A093VKV7
J	Cell wall antigen	protein	133	85% helix, 0% strand	A0A093VKV7

Ligands and binding sites

ACD · Arachidonic acid · ligand · 4 copies · chains B, I, J

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	445	0.86	0.93	55	ACD
2	418	0.86	0.93	55	empty
3	432	0.86	0.93	54	empty
4	341	0.85	0.94	39	empty
5	310	0.85	0.94	42	empty

Interfaces

19 interfaces between chains.

A–H · 553 Å² buried · 2 hydrogen bonds · protein-protein
B–I · 550 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 443 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 392 Å² buried · 2 hydrogen bonds · protein-protein
B–J · 373 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5ECF · Ligand binding domain 1 of Penicillium marneffei MP1 protein complexed with arachidonic… · 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 A0A093VKV7
Elsewhere: RCSB PDB 5ECF · PDBe 5ECF · UniProt A0A093VKV7

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