MolNFT v1 · #39324 · protein

Crystal structure of a small single-stranded DNA binding protein from mycoplasma pneumoniae

2HQL · Hypothetical protein MG376 homolog: “Crystal structure of a small single-stranded DNA binding protein from mycoplasma pneumoniae”. X-ray diffraction, 7 pockets (best druggability 0.52). MolNFT v1 #39324 on GenesisL1: 3D structure…

PDB: 2HQL
Type: protein
Length: 594 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein MG376 homolog
UniProt: P75224
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Hypothetical protein MG376 homolog	protein	104	11% helix, 60% strand	P75224
B	Hypothetical protein MG376 homolog	protein	101	13% helix, 61% strand	P75224
C	Hypothetical protein MG376 homolog	protein	91	11% helix, 57% strand	P75224
E	Hypothetical protein MG376 homolog	protein	98	14% helix, 57% strand	P75224
F	Hypothetical protein MG376 homolog	protein	96	10% helix, 47% strand	P75224

Pockets

7 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	163	0.52	0.78	31	empty
2	207	0.51	0.76	43	empty
3	61	0.42	0.81	16	empty
4	131	0.41	0.75	17	empty
5	57	0.28	0.74	12	empty

Interfaces

6 interfaces between chains.

D–F · 1962 Å² buried · 38 hydrogen bonds · protein-protein
A–E · 1647 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 1395 Å² buried · 28 hydrogen bonds · protein-protein
B–E · 296 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 189 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2HQL · Crystal structure of a small single-stranded DNA binding protein from Mycoplasma… · the same entry in another collection · chain F against F, TM-score 1.00
P75224 · AlphaFold monomer V2.0 prediction for uncharacterized protein MG376 homolog (P75224) · a predicted model of the same protein · chain C against A, TM-score 0.93

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 P75224
Elsewhere: RCSB PDB 2HQL · PDBe 2HQL · UniProt P75224

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