MolNFT v1 · #126379 · protein

Crystal structure of PBP2A from mrsa in the presence of ceftazidime ligand

5M1A · Penicillin-binding protein 2: “Crystal structure of PBP2A from mrsa in the presence of ceftazidime ligand”. X-ray diffraction, 2 ligands (MUR, CD), 14 pockets (best druggability 0.77). MolNFT v1 #126379 on GenesisL1: 3D structure…

PDB: 5M1A
Type: protein
Length: 1,274 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin-binding protein 2
UniProt: E2D9B8
Ligands: MUR, CD
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Penicillin-binding protein 2	protein	639	34% helix, 27% strand	E2D9B8
B	Penicillin-binding protein 2	protein	635	36% helix, 27% strand	E2D9B8

Ligands and binding sites

MUR · beta-muramic acid · ligand · 2 copies · chains A, B
CD · Cadmium ion · metal · 6 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1085	0.77	0.79	117	CD, MUR
2	461	0.65	0.78	51	empty
3	334	0.61	0.78	37	empty
4	228	0.56	0.78	29	MUR
5	149	0.56	0.81	26	empty

Interfaces

1 interface between chains.

A–B · 1640 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

5M1A · Crystal structure of PBP2a from MRSA in the presence of Ceftazidime ligand · 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 E2D9B8
Elsewhere: RCSB PDB 5M1A · PDBe 5M1A · UniProt E2D9B8

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