MolNFT v1 · #103770 · protein

C-terminal domain of DNA binding protein

4PQK · Maltose ABC transporter periplasmic protein, truncated…: “C-terminal domain of DNA binding protein”. X-ray diffraction, 1 ligand (GLC), 20 pockets (best druggability 0.76). MolNFT v1 #103770 on GenesisL1: 3D structure, binding sites…

PDB: 4PQK
Type: protein
Length: 1,905 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose ABC transporter periplasmic protein, truncated replication protein repa
UniProt: U6NJU2, B1B3N6
Ligands: GLC
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose ABC transporter periplasmic protein, truncated replication protein repa	protein	478	52% helix, 14% strand	U6NJU2, B1B3N6
B	Maltose ABC transporter periplasmic protein, truncated replication protein repa	protein	479	49% helix, 16% strand	U6NJU2, B1B3N6
C	Maltose ABC transporter periplasmic protein, truncated replication protein repa	protein	476	50% helix, 16% strand	U6NJU2, B1B3N6
D	Maltose ABC transporter periplasmic protein, truncated replication protein repa	protein	472	49% helix, 16% strand	U6NJU2, B1B3N6

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1065	0.76	0.78	83	GLC
2	391	0.74	0.84	35	GLC
3	587	0.74	0.81	52	GLC
4	477	0.72	0.82	41	GLC
5	609	0.70	0.78	67	empty

Interfaces

5 interfaces between chains.

B–C · 322 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 267 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 250 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 100 Å² buried · 1 hydrogen bond · protein-protein
C–D · 100 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4PQK · C-Terminal domain of DNA binding protein · 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 U6NJU2
Every structure of UniProt B1B3N6
Elsewhere: RCSB PDB 4PQK · PDBe 4PQK · UniProt U6NJU2 · UniProt B1B3N6

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