SMTL ID : 3n33.1

Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with pefabloc SC (AEBSF)

Coordinates

PDB Format

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 C: M.262, H.264, N.314, D.315 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.314, C:D.315, A:G.89, A:Q.90, A:H.299 GOL.10: 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:G.89, B:Q.90, B:H.299, D:N.314, D:D.315, D:D.315 GOL.17: 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 A, 3 interactions with chain C Hydrogen bonds: A:N.314, A:D.315, A:D.315, C:G.89, C:Q.90, C:H.299 GOL.25: 11 residues within 4Å: Chain B: 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 B Hydrogen bonds: D:G.89, D:Q.90, D:H.299, B:N.314, B:D.315

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 9 residues within 4Å: Chain A: P.119, E.121, A.122, F.124, S.125, L.303, G.304 Chain C: T.316 Ligands: AES.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:G.304 Hydrogen bonds: C:T.316 EPE.11: 9 residues within 4Å: Chain A: L.287 Chain B: E.121, A.122, F.124, S.125, L.303, G.304 Chain D: T.316 Ligands: AES.3 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.90, B:P.302, B:G.304

8 x AES: 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE(Non-covalent)

AES.3: 13 residues within 4Å: Chain A: T.76, G.77, T.100, E.133, S.250, L.287 Chain B: L.84, L.92, F.124, S.125, L.128 Ligands: SO4.9, EPE.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.76, A:S.250 Hydrophobic interactions: B:L.128 pi-Stacking: B:F.124 AES.4: 9 residues within 4Å: Chain A: E.120, L.123, F.124, L.127 Chain B: M.41, L.135, N.137, V.142, F.143 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:E.120, A:L.123, B:F.143 Hydrogen bonds: A:E.120 AES.12: 12 residues within 4Å: Chain A: L.84, L.92, F.124, S.125, L.128 Chain B: T.76, G.77, E.133, S.250, L.287 Ligands: EPE.2, SO4.16 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.287 Hydrogen bonds: B:E.133, B:S.250 Water bridges: B:G.289 pi-Stacking: A:F.124 AES.13: 9 residues within 4Å: Chain A: M.41, L.135, N.137, V.142, F.143 Chain B: E.120, L.123, F.124, L.127 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.120 AES.18: 11 residues within 4Å: Chain C: T.76, G.77, E.133, S.250, L.287 Chain D: L.84, L.92, F.124, S.125, L.128 Ligands: SO4.24 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.133, C:S.250 pi-Stacking: D:F.124 AES.19: 9 residues within 4Å: Chain C: E.120, L.123, F.124, L.127 Chain D: M.41, L.135, N.137, V.142, F.143 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.143, C:E.120 Hydrogen bonds: C:E.120 AES.26: 13 residues within 4Å: Chain C: L.84, L.92, F.124, S.125, L.128 Chain D: T.76, G.77, T.100, E.133, S.250, L.287 Ligands: SO4.23, SO4.30 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.287 Hydrogen bonds: D:E.133, D:S.250 pi-Stacking: C:F.124 AES.27: 10 residues within 4Å: Chain C: M.41, I.43, L.135, N.137, V.142, F.143 Chain D: E.120, L.123, F.124, L.127 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:E.120, D:L.123, C:F.143

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

SO4.5: 8 residues within 4Å: Chain A: R.138, I.176, P.230, E.231, V.232, A.237, A.352, V.354 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: D.112, V.115 Chain B: I.43, F.143, H.145 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: G.285, A.286, L.287, S.288 Chain D: S.318, N.322 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: I.43, F.143, H.145 Chain B: D.112, V.115 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain A: T.134, L.135, N.207, S.250, L.287, S.288 Ligands: AES.3 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain B: R.138, I.176, P.230, E.231, V.232, A.237, A.352, V.354 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain B: G.285, A.286, L.287, S.288 Chain C: S.318, N.322 Ligand excluded by PLIP SO4.16: 7 residues within 4Å: Chain B: T.134, L.135, N.207, S.250, L.287, S.288 Ligands: AES.12 Ligand excluded by PLIP SO4.20: 8 residues within 4Å: Chain C: R.138, I.176, P.230, E.231, V.232, A.237, A.352, V.354 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: D.112, V.115 Chain D: I.43, F.143, H.145 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain B: S.318, N.322 Chain C: G.285, A.286, L.287, S.288 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain A: T.316 Chain C: F.124, S.125, L.303 Chain D: L.287 Ligands: AES.26 Ligand excluded by PLIP SO4.24: 7 residues within 4Å: Chain C: T.134, L.135, N.207, S.250, L.287, S.288 Ligands: AES.18 Ligand excluded by PLIP SO4.28: 7 residues within 4Å: Chain D: R.138, P.230, E.231, V.232, A.237, A.352, V.354 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain A: S.318, N.322 Chain D: G.285, A.286, L.287, S.288 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain D: T.134, L.135, N.207, S.250, L.287, S.288 Ligands: AES.26 Ligand excluded by PLIP

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

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