MolNFT v1 · #114850 · protein

Crystal structure of zn-bound hlyd from E. COLI

5C22 · Chromosomal hemolysin D: “Crystal structure of zn-bound hlyd from E. COLI”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #114850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C22
Type: protein
Length: 1,053 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chromosomal hemolysin D
UniProt: O87505
Ligands: ZN
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 66% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Chromosomal hemolysin D	protein	266	64% helix, 12% strand	O87505
B	Chromosomal hemolysin D	protein	267	65% helix, 12% strand	O87505
C	Chromosomal hemolysin D	protein	254	69% helix, 8% strand	O87505

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	298	0.68	0.83	28	empty
2	257	0.66	0.83	28	empty
3	54	0.25	0.73	12	empty

Interfaces

2 interfaces between chains.

B–C · 867 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 860 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5C22 · Crystal structure of Zn-bound HlyD from E. coli · the same entry in another collection · chain C against C, 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 O87505
Elsewhere: RCSB PDB 5C22 · PDBe 5C22 · UniProt O87505

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