SMTL ID : 3n5i.1

Crystal structure of the precursor (S250A mutant) of the N-terminal beta-aminopeptidase BapA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: V.88, G.89, Q.90, P.263, H.299, I.301, P.307 Chain D: M.262, H.264, N.314, D.315 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:N.314, D:D.315, D:D.315, A:V.88, A:Q.90, A:H.299 GOL.2: 11 residues within 4Å: Chain A: M.262, H.264, N.314, D.315 Chain D: V.88, G.89, Q.90, P.263, H.299, I.301, P.307 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:V.88, D:Q.90, D:H.299, A:N.314, A:D.315, A:D.315 GOL.3: 13 residues within 4Å: Chain B: M.262, H.264, Q.265, I.313, N.314, D.315 Chain C: V.88, G.89, Q.90, P.263, H.299, I.301, P.307 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.314, B:D.315, C:V.88, C:Q.90, C:H.299 GOL.5: 11 residues within 4Å: Chain B: V.88, G.89, Q.90, P.263, H.299, I.301, P.307 Chain C: M.262, H.264, N.314, D.315 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:V.88, B:Q.90, B:H.299, C:N.314, C:D.315

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain B: G.13, T.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.14, B:T.14 Water bridges: B:T.14, B:T.14, B:S.192, B:Q.330 SO4.6: 3 residues within 4Å: Chain D: P.302, G.305, R.308 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.306, D:K.306 SO4.7: 3 residues within 4Å: Chain D: G.39, A.40, N.351 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.40, D:N.351 Water bridges: D:D.38, D:A.40 SO4.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.9: 2 residues within 4Å: Chain D: G.13, T.14 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.14, D:T.14 Water bridges: D:G.13, D:T.14, D:T.14, D:R.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Merz, T. et al., Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family. Structure (2012)

Release Date

2011-06-08

Peptides

Beta-peptidyl aminopeptidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-peptidyl aminopeptidase