MolNFT v1 · #128291 · protein

NB36 SER85CYS with hg, crystal form 1

5NM0: “NB36 SER85CYS with hg, crystal form 1”. X-ray diffraction, 1 ligand (HG), 2 pockets (best druggability 0.53). MolNFT v1 #128291 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NM0
Type: protein
Length: 462 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NB36
Ligands: HG
Pockets: 2 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NB36	protein	117	9% helix, 47% strand	—
B	NB36	protein	118	8% helix, 47% strand	—
C	NB36	protein	111	9% helix, 48% strand	—
D	NB36	protein	116	11% helix, 46% strand	—

Ligands and binding sites

HG · Mercury (II) ion · metal · 2 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.53	0.83	19	empty
2	136	0.45	0.77	24	empty

Interfaces

3 interfaces between chains.

C–D · 722 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 360 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 359 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5NM0 · Nb36 Ser85Cys with Hg, crystal form 1 · 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
Elsewhere: RCSB PDB 5NM0 · PDBe 5NM0

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