SMTL ID : 3nfb.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 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 B: M.262, H.264, N.314, D.315 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.88, A:Q.90, A:H.299, B:N.314, B:D.315 GOL.2: 11 residues within 4Å: Chain A: M.262, H.264, N.314, D.315 Chain B: V.88, G.89, Q.90, P.263, H.299, I.301, P.307 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.314, A:D.315, A:D.315, B:G.89, B:Q.90, B:H.299 GOL.8: 11 residues within 4Å: Chain C: M.262, H.264, N.314, D.315 Chain D: V.88, G.89, Q.90, P.263, H.299, I.301, P.307 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:V.88, D:Q.90, D:H.299, C:N.314, C:D.315 GOL.9: 11 residues within 4Å: Chain C: 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 C Hydrogen bonds: D:N.314, D:D.315, D:D.315, C:G.89, C:Q.90, C:H.299

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

OAE.3: 13 residues within 4Å: Chain A: T.76, G.77, E.133, T.134, L.135, N.137, N.207, S.250, L.287 Chain C: F.124, L.127, L.128 Ligands: SO4.5 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.135, A:L.287, C:F.124, C:L.127, C:L.128, C:L.128 Hydrogen bonds: A:E.133, A:L.135, A:N.207, A:S.250, A:S.250, A:L.287 Water bridges: A:N.137, A:N.137 OAE.4: 5 residues within 4Å: Chain A: R.138, P.230, V.232, A.237, A.238 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.230, A:V.232, A:V.232, A:A.237 Hydrogen bonds: A:A.237 Water bridges: A:R.138, A:R.138, A:T.179 Salt bridges: A:R.138 OAE.6: 14 residues within 4Å: Chain B: T.76, G.77, T.100, E.133, T.134, L.135, N.137, N.207, S.250, L.287 Chain D: F.124, L.127, L.128 Ligands: SO4.11 16 PLIP interactions: 4 interactions with chain D, 12 interactions with chain B Hydrophobic interactions: D:F.124, D:L.127, D:L.128, D:L.128, B:T.100, B:L.135, B:L.287 Hydrogen bonds: B:E.133, B:L.135, B:N.207, B:S.250, B:S.250, B:L.287 Water bridges: B:L.135, B:N.137, B:L.287 OAE.10: 14 residues within 4Å: Chain A: F.124, L.127, L.128 Chain C: T.76, G.77, T.100, E.133, T.134, L.135, N.137, N.207, S.250, L.287 Ligands: SO4.7 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain C Hydrophobic interactions: A:F.124, A:L.127, A:L.128, A:L.128, C:T.100, C:L.135, C:L.287 Hydrogen bonds: C:E.133, C:L.135, C:N.207, C:S.250, C:S.250, C:L.287 Water bridges: C:L.135, C:N.137, C:G.289 OAE.12: 13 residues within 4Å: Chain B: F.124, L.127, L.128 Chain D: T.76, G.77, E.133, T.134, L.135, N.137, N.207, S.250, L.287 Ligands: SO4.14 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:L.287, B:F.124, B:L.127, B:L.128, B:L.128 Hydrogen bonds: D:E.133, D:L.135, D:N.207, D:S.250, D:S.250, D:L.287 Water bridges: D:L.135, D:N.137, D:N.137 OAE.13: 5 residues within 4Å: Chain D: R.138, P.230, V.232, A.237, A.238 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:P.230, D:V.232, D:A.237 Hydrogen bonds: D:A.237 Water bridges: D:R.138, D:T.179, D:D.210, D:G.239, D:G.239 Salt bridges: D:R.138

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

SO4.5: 7 residues within 4Å: Chain A: G.285, A.286, L.287, S.288 Chain D: S.318, N.322 Ligands: OAE.3 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:S.318, D:S.318, D:N.322, A:L.287 Water bridges: A:S.250, A:S.288, A:S.288, A:S.288 SO4.7: 7 residues within 4Å: Chain B: S.318, N.322 Chain C: G.285, A.286, L.287, S.288 Ligands: OAE.10 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.286, C:L.287, B:S.318, B:N.322 Water bridges: C:G.285, C:G.285, C:S.288 SO4.11: 7 residues within 4Å: Chain B: G.285, A.286, L.287, S.288 Chain C: S.318, N.322 Ligands: OAE.6 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:A.286, B:L.287, C:S.318, C:S.318, C:N.322 Water bridges: B:G.285, B:G.285, B:S.288, B:S.288 SO4.14: 7 residues within 4Å: Chain A: S.318, N.322 Chain D: G.285, A.286, L.287, S.288 Ligands: OAE.12 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:G.285, D:L.287, A:S.318, A:S.318, A:N.322 Water bridges: D:S.250, D:G.285, D:G.285, D:S.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heck, T. et al., Crystal structure 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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