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Crystal structure of stabilized tem-1 beta-lactamase variant V.13

Analyse Crystal structure of stabilized tem-1 beta-lactamase variant V.13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IBX
Type: protein
Length: 1,315 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase tem
EC: 3.5.2.6
UniProt: P62593
Ligands: CA, SO4
Pockets: 10 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Beta-lactamase tem (EC 3.5.2.6)	protein	263	43% helix, 17% strand	P62593

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B, C
SO4 · Sulfate ion · ion · chains C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, D

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

Pockets

10 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	439	0.70	0.81	67	empty
2	302	0.59	0.78	47	SO4
3	217	0.43	0.72	25	empty
4	174	0.40	0.72	33	empty
5	61	0.36	0.79	20	empty

Interfaces

6 interfaces between chains.

A–B · 516 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 470 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 445 Å² buried · 9 hydrogen bonds · protein-protein
B–E · 75 Å² buried · 0 hydrogen bonds · protein-protein
A–E · 71 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4IBX · Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 · the same entry in another collection · chain E against E, TM-score 1.00
P62593 · AlphaFold monomer V2.0 prediction for beta-lactamase tem (P62593) · a predicted model of the same protein · 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 P62593
Elsewhere: RCSB PDB 4IBX · PDBe 4IBX · UniProt P62593

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