SMTL ID : 3kl9.1

Crystal structure of PepA from Streptococcus pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-12-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.67, D.182, N.183, E.214, E.215, D.237 Ligands: ZN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.182, A:D.237, A:D.237 ZN.2: 5 residues within 4Å: Chain A: D.182, E.214, E.215, H.319 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.182, A:E.215, A:E.215, A:H.319 ZN.3: 6 residues within 4Å: Chain B: H.67, D.182, E.214, D.237, C.238 Ligands: ZN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.182, B:D.237, B:D.237 ZN.4: 5 residues within 4Å: Chain B: D.182, E.214, E.215, H.319 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.182, B:E.215, B:E.215, B:H.319 ZN.5: 5 residues within 4Å: Chain C: H.67, D.182, E.214, D.237 Ligands: ZN.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.182, C:D.237, C:D.237 ZN.6: 4 residues within 4Å: Chain C: D.182, E.215, H.319 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.182, C:E.215, C:E.215, C:H.319 ZN.7: 4 residues within 4Å: Chain D: D.182, E.215, H.319 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.182, D:E.215, D:E.215, D:H.319 ZN.8: 5 residues within 4Å: Chain D: H.67, D.182, E.214, D.237 Ligands: ZN.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.182, D:D.237 ZN.9: 5 residues within 4Å: Chain E: D.182, E.214, E.215, H.319 Ligands: ZN.10 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.182, E:E.215, E:E.215, E:H.319 ZN.10: 5 residues within 4Å: Chain E: H.67, D.182, E.214, D.237 Ligands: ZN.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.182, E:D.237, E:D.237 ZN.11: 5 residues within 4Å: Chain F: H.67, D.182, E.214, D.237 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.182, F:D.237, F:D.237 ZN.12: 5 residues within 4Å: Chain F: D.182, E.214, E.215, H.319 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.182, F:E.215, F:E.215, F:H.319 ZN.13: 6 residues within 4Å: Chain G: H.67, D.182, E.214, D.237, C.238 Ligands: ZN.14 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.182, G:D.237, G:D.237 ZN.14: 5 residues within 4Å: Chain G: D.182, E.214, E.215, H.319 Ligands: ZN.13 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.182, G:E.215, G:E.215, G:H.319 ZN.15: 5 residues within 4Å: Chain H: H.67, D.182, E.214, D.237 Ligands: ZN.16 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.182, H:D.237, H:D.237 ZN.16: 5 residues within 4Å: Chain H: D.182, E.214, E.215, H.319 Ligands: ZN.15 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.182, H:E.215, H:E.215, H:H.319 ZN.17: 5 residues within 4Å: Chain I: H.67, D.182, E.214, D.237 Ligands: ZN.18 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.182, I:D.237, I:D.237 ZN.18: 5 residues within 4Å: Chain I: D.182, E.214, E.215, H.319 Ligands: ZN.17 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:D.182, I:E.215, I:E.215, I:H.319 ZN.19: 5 residues within 4Å: Chain J: H.67, D.182, E.214, D.237 Ligands: ZN.20 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:D.182, J:D.237, J:D.237 ZN.20: 5 residues within 4Å: Chain J: D.182, E.214, E.215, H.319 Ligands: ZN.19 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.182, J:E.215, J:E.215, J:H.319 ZN.21: 5 residues within 4Å: Chain K: D.182, E.214, E.215, H.319 Ligands: ZN.22 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.182, K:E.215, K:E.215, K:H.319 ZN.22: 5 residues within 4Å: Chain K: H.67, D.182, E.214, D.237 Ligands: ZN.21 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.182, K:D.237, K:D.237 ZN.23: 5 residues within 4Å: Chain L: H.67, D.182, E.214, D.237 Ligands: ZN.24 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.182, L:D.237, L:D.237 ZN.24: 4 residues within 4Å: Chain L: D.182, E.215, H.319 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.182, L:E.215, L:E.215, L:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, D. et al., Structural basis for the substrate specificity of PepA from Streptococcus pneumoniae, a dodecameric tetrahedral protease. Biochem.Biophys.Res.Commun. (2010)

Release Date

2010-02-02

Peptides

Glutamyl aminopeptidase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Glutamyl aminopeptidase