MolNFT v1 · #155554 · protein

Magnesium ion-bound sspb crystal structure

6LB9 · DUF4007 domain-containing protein: “Magnesium ion-bound sspb crystal structure”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.77). MolNFT v1 #155554 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LB9
Type: protein
Length: 689 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DUF4007 domain-containing protein
UniProt: B5GPM3
Ligands: MG
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DUF4007 domain-containing protein	protein	345	49% helix, 12% strand	B5GPM3
B	DUF4007 domain-containing protein	protein	344	49% helix, 11% strand	B5GPM3

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.77	0.97	21	empty
2	267	0.67	0.83	34	empty
3	295	0.67	0.82	40	empty
4	204	0.60	0.82	35	empty
5	173	0.45	0.75	27	empty

Interfaces

1 interface between chains.

A–B · 1347 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6LB9 · Magnesium ion-bound SspB crystal structure · 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 B5GPM3
Elsewhere: RCSB PDB 6LB9 · PDBe 6LB9 · UniProt B5GPM3

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