SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 16

Table 1.4 Result of SuMo run using the CES binding site of the Penicillin Binding Protein
(1QMF) as reference against all the proteins of the Protein Data Bank ( PDB ). Only the first 45
entries are displayed. The white to light grays entries are all penicillin binding proteins ( PBP ).
The dark grays entries are beta-lactamase proteins
Hit Id PDB Id SCF Count Sumo Score Header line of the PDB structure

1 1QMF 67 33.02 Penicillin-binding protein 2X

(PBP-2X)

2 2ZC3 51 28.15 Penicillin-binding protein 2X

(PBP 2X)

3 2ZC4 50 27.16 Penicillin-binding protein 2X

(PBP 2X)

4 1QME 50 27.01 Penicillin-binding protein 2X

(PBP-2X)

5 2Z2L 48 26.95 Penicillin-binding protein 2X

(PBP2X)

6 2Z2M 43 24.96 Cefditoren-acylated penicillin-

binding protein 2X

7 1RP5 48 23.615 PBP2X from Streptococcus

pneumoniae strain 5259
WITH REDUCED suscepti-
bility to beta-lactam
antibiotics

8 1PYY 43 22.89 Double mutant PBP2X T338A/

M339F from Streptococcus
pneumoniae strain R6 AT 2.4
A resolution

9 2WAF 34 19.23 Penicillin-binding protein 2B

(PBP-2B)

10 2WAD 30 16.61 Penicillin-binding protein 2B

(PBP-2B)

11 2WAE 31 16.57 Penicillin-binding protein 2B

(PBP-2B)

12 2ZC5 27 14.09 Penicillin-binding protein 1A

(PBP 1A) acyl-enzyme
complex (Biapenem)

13 2C5W 25 13.91 Penicillin-binding protein 1A

(PBP-1A) acyl-enzyme
complex (Cefotaxime)

14 2ZC6 25 13.30 Penicillin-binding protein 1A

(PBP 1A) acyl-enzyme
complex (Tebipenem)

15 2JE5 24 13.25 Structural and mechanistic basis

of penicillin binding protein
inhibition by lactivicins

16 2JCH 22 12.71 Structural and mechanistic basis

of penicillin binding protein
inhibition by lactivicins
(continued)