SMTL ID : 3n2w.1

Crystal structure of the N-terminal beta-aminopeptidase BapA from Sphingosinicella xenopeptidilytica

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 16 residues within 4Å: Chain A: A.67, V.88, G.89, Q.90, P.263, H.299, I.301, P.307 Chain D: M.262, H.264, Q.265, I.312, I.313, N.314, D.315, T.316 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.264, D:N.314, D:D.315, D:D.315, A:Q.90, A:H.299 GOL.2: 11 residues within 4Å: Chain A: L.84, L.92, F.124, S.125, R.126, L.127, L.128, L.303 Chain B: T.76, L.287 Chain D: T.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.124, A:L.127, A:L.128 GOL.5: 16 residues within 4Å: Chain B: A.67, V.88, G.89, Q.90, P.263, H.299, I.301, P.307 Chain C: M.262, H.264, Q.265, I.312, I.313, N.314, D.315, T.316 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Q.90, B:H.299, C:H.264, C:N.314, C:D.315 GOL.6: 16 residues within 4Å: Chain B: M.262, H.264, Q.265, I.312, I.313, N.314, D.315, T.316 Chain C: A.67, V.88, G.89, Q.90, P.263, H.299, I.301, P.307 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.264, B:N.314, B:D.315, B:D.315, C:Q.90, C:H.299 GOL.7: 14 residues within 4Å: Chain C: T.76, G.77, E.78, T.100, E.133, T.134, L.135, S.250, L.287, G.289 Chain D: L.127, L.128 Ligands: SO4.11, GOL.13 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.100, C:T.100, C:E.133, C:L.135, C:L.287 Water bridges: C:G.289 GOL.8: 9 residues within 4Å: Chain B: T.316 Chain C: L.84, L.92, F.124, S.125, R.126, L.127, L.128 Chain D: L.287 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.124, C:L.127, C:L.128 GOL.12: 16 residues within 4Å: Chain A: M.262, H.264, Q.265, I.312, I.313, N.314, D.315, T.316 Chain D: A.67, V.88, G.89, Q.90, P.263, H.299, I.301, P.307 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:H.264, A:N.314, A:D.315, A:D.315, D:Q.90, D:H.299 GOL.13: 11 residues within 4Å: Chain A: T.316 Chain C: L.287 Chain D: L.84, L.92, F.124, S.125, R.126, L.127, L.128, L.303 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.124, D:L.127, D:L.128

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

SO4.3: 6 residues within 4Å: Chain A: G.285, A.286, L.287, S.288 Chain C: S.318, N.322 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.286, A:L.287, C:S.318, C:N.322 Water bridges: A:S.250, A:S.288 SO4.4: 6 residues within 4Å: Chain A: V.219, E.224, I.365, A.368, R.369 Chain C: R.369 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.224, C:R.369 SO4.9: 6 residues within 4Å: Chain A: S.318, N.322 Chain C: G.285, A.286, L.287, S.288 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:A.286, C:L.287, A:S.318, A:N.322 Water bridges: C:L.287, C:S.288, C:S.288, C:S.288 SO4.10: 7 residues within 4Å: Chain B: K.306, P.307 Chain C: I.312, I.313, N.314, D.317, T.320 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.305, C:N.314, C:T.320 Water bridges: C:N.314 SO4.11: 8 residues within 4Å: Chain C: T.134, L.135, N.207, S.250, L.287, S.288, G.289 Ligands: GOL.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:L.135, C:N.207, C:S.250, C:S.250 Water bridges: C:N.207, C:N.207, C:S.250, C:L.287 SO4.14: 6 residues within 4Å: Chain B: S.318, N.322 Chain D: G.285, A.286, L.287, S.288 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:N.322, D:A.286, D:L.287 Water bridges: D:G.285 SO4.15: 2 residues within 4Å: Chain D: G.13, T.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.14, D:T.14 Water bridges: D:T.14, D:T.14, D:S.192, D:R.326, 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

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