MolNFT v1 · #121433 · protein

Crystal structure of TEM1 beta-lactamase

5HVI · Beta-lactamase tem: “Crystal structure of TEM1 beta-lactamase”. X-ray diffraction, 9 pockets (best druggability 0.77). MolNFT v1 #121433 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HVI
Type: protein
Length: 1,052 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase tem
EC: 3.5.2.6
UniProt: P62593
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-lactamase tem (EC 3.5.2.6)	protein	263	45% helix, 17% strand	P62593

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1075	0.77	0.79	95	empty
2	919	0.76	0.79	85	empty
3	308	0.53	0.75	38	empty
4	76	0.45	0.82	22	empty
5	66	0.40	0.80	21	empty

Interfaces

5 interfaces between chains.

A–B · 664 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 482 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 254 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 225 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 69 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5HVI · Crystal structure of TEM1 beta-lactamase · the same entry in another collection · chain D against D, TM-score 1.00
P62593 · AlphaFold monomer V2.0 prediction for beta-lactamase tem (P62593) · a predicted model of the same protein · chain B 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 P62593
Elsewhere: RCSB PDB 5HVI · PDBe 5HVI · UniProt P62593

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