MolNFT v1 · #154834 · protein

Crystal structure of the metallo-beta-lactamase fold protein yhfi from bacillus subtilis (space group P4332)

6KNT · Putative metal-dependent hydrolase: “Crystal structure of the metallo-beta-lactamase fold protein yhfi from bacillus subtilis (space group P4332)”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.82). MolNFT v1…

PDB: 6KNT
Type: protein
Length: 979 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative metal-dependent hydrolase
UniProt: E0TYN8
Ligands: ZN
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative metal-dependent hydrolase	protein	246	23% helix, 31% strand	E0TYN8
B	Putative metal-dependent hydrolase	protein	245	23% helix, 30% strand	E0TYN8
C, D	Putative metal-dependent hydrolase	protein	244	21% helix, 30% strand	E0TYN8

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	179	0.82	0.96	28	empty
2	177	0.81	0.96	28	empty
3	121	0.72	0.93	29	empty
4	115	0.72	0.93	28	empty
5	462	0.69	0.80	47	empty

Interfaces

6 interfaces between chains.

C–D · 1202 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1164 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 469 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 446 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 431 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6KNT · Crystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis… · 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 E0TYN8
Elsewhere: RCSB PDB 6KNT · PDBe 6KNT · UniProt E0TYN8

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