MolNFT v1 · #1957 · protein + DNA

Restriction endonuclease bamhi complex with DNA

1BHM · DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)- 3'): “Restriction endonuclease bamhi complex with DNA”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1 #1957 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1BHM
Type: protein + DNA
Length: 429 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)- 3'); Protein (bamhi (E.C.3.1.21.4))
EC: 3.1.21.4
UniProt: P23940
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA (5'-D(TPAPTPGPGPAPTPCPCPAPTPA)- 3')	dna	12	—	—
D	DNA (5'-D(TPAPTPGPGPAPTPCPCPAPTPA)- 3')	dna	11	—	—
A	Protein (bamhi (E.C.3.1.21.4)) (EC 3.1.21.4)	protein	198	37% helix, 27% strand	P23940
B	Protein (bamhi (E.C.3.1.21.4)) (EC 3.1.21.4)	protein	208	38% helix, 27% strand	P23940

Pockets

5 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	517	0.71	0.81	29	empty
2	77	0.69	0.95	16	empty
3	94	0.61	0.88	16	empty
4	304	0.54	0.76	29	empty
5	106	0.38	0.75	18	empty

Interfaces

6 interfaces between chains.

A–B · 1053 Å² buried · 13 hydrogen bonds · protein-protein
D–A · 856 Å² buried · 18 hydrogen bonds · protein-nucleic
C–B · 676 Å² buried · 16 hydrogen bonds · protein-nucleic
C–D · 566 Å² buried · 47 hydrogen bonds · nucleic-nucleic
C–A · 501 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

1BHM · Restriction endonuclease bamhi complex with DNA · the same entry in another collection · chain A against A, TM-score 1.00
P23940 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme bamhi (P23940) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P23940
Elsewhere: RCSB PDB 1BHM · PDBe 1BHM · UniProt P23940

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