SMTL ID : 3ndv.1

Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with ampicillin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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 C: M.262, H.264, N.314, D.315 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:V.88, A:Q.90, A:H.299, C:N.314, C:D.315 GOL.4: 11 residues within 4Å: Chain B: 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 B, 3 interactions with chain D Hydrogen bonds: B:V.88, B:Q.90, B:H.299, D:N.314, D:D.315, D:D.315 GOL.5: 12 residues within 4Å: Chain B: M.262, H.264, I.313, 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 B, 3 interactions with chain D Hydrogen bonds: B:Q.265, B:N.314, B:D.315, D:V.88, D:Q.90, D:H.299 GOL.7: 11 residues within 4Å: Chain A: M.262, H.264, N.314, D.315 Chain C: V.88, G.89, Q.90, P.263, H.299, I.301, P.307 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:V.88, C:Q.90, C:H.299, A:N.314, A:D.315, A:D.315

4 x AIC: (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID(Non-covalent)

AIC.2: 16 residues within 4Å: Chain A: T.76, G.77, T.100, E.133, T.134, L.135, N.137, R.138, N.207, S.250, L.287, S.288 Chain B: F.124, L.127, L.128 Ligands: NDV.3 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:L.127, B:L.128, B:L.128, A:T.100, A:L.287 Hydrogen bonds: A:L.135, A:N.207, A:S.250, A:S.250, A:L.287 Water bridges: A:N.137, A:S.250 Salt bridges: A:R.138 AIC.6: 15 residues within 4Å: Chain A: F.124, L.127, L.128 Chain B: T.76, G.77, T.100, E.133, T.134, L.135, N.137, R.138, N.207, S.250, L.287, S.288 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.100, B:L.287, A:L.127, A:L.128 Hydrogen bonds: B:L.135, B:N.137, B:N.207, B:S.250, B:S.250, B:S.250, B:L.287 Water bridges: B:L.287, B:S.288 Salt bridges: B:R.138 AIC.8: 15 residues within 4Å: Chain C: T.76, G.77, T.100, E.133, T.134, L.135, N.137, R.138, N.207, S.250, L.287, S.288 Chain D: F.124, L.127, L.128 12 PLIP interactions: 2 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:L.127, D:L.128, C:T.100, C:L.287 Hydrogen bonds: C:L.135, C:N.137, C:N.207, C:S.250, C:S.250, C:L.287 Water bridges: C:L.287 Salt bridges: C:R.138 AIC.9: 16 residues within 4Å: Chain C: F.124, L.127, L.128 Chain D: T.76, G.77, T.100, E.133, T.134, L.135, N.137, R.138, N.207, S.250, L.287, S.288 Ligands: NDV.10 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:T.100, D:L.287, C:L.127, C:L.128, C:L.128 Hydrogen bonds: D:L.135, D:N.207, D:S.250, D:S.250, D:S.250, D:L.287 Water bridges: D:N.137, D:S.288, D:G.289 Salt bridges: D:R.138

2 x NDV: (2S,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

NDV.3: 6 residues within 4Å: Chain A: R.138, E.231, V.232, A.237, A.238 Ligands: AIC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.232, A:A.237 Hydrogen bonds: A:R.138 Salt bridges: A:R.138 pi-Cation interactions: A:R.138 NDV.10: 6 residues within 4Å: Chain D: R.138, I.176, V.232, A.237, A.238 Ligands: AIC.9 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.176, D:V.232, D:A.237 Salt bridges: D:R.138 pi-Cation interactions: D:R.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heck, T. et al., Crystal structures and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family. To be Published

Release Date

2011-09-28

Peptides

Beta-peptidyl aminopeptidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-peptidyl aminopeptidase

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