MolNFT v1 · #138513 · protein

De novo design of polynuclear transition metal clusters in helix bundles-4DH2

5WLM · Helical bundle 4DH2: “De novo design of polynuclear transition metal clusters in helix bundles-4DH2”. X-ray diffraction, 3 ligands (ACE, ZN, NH2). MolNFT v1 #138513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WLM
Type: protein
Length: 104 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Helical bundle 4DH2
Ligands: ACE, ZN, NH2

Structure

x-ray diffraction · 1 distinct chain · 92% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Helical bundle 4DH2	protein	26	92% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 4 copies · chains A, B, D, C
ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
NH2 · Amino group · ion · 4 copies · chains A, C, B, D

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

Interfaces

6 interfaces between chains.

A–B · 744 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 732 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 100 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 90 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 51 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5WLM · De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2 · 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 5WLM · PDBe 5WLM

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