SMTL ID : 1gm9.1

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: T.150, S.151, E.152, I.153, D.154 Chain B: I.77, L.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.151, A:I.153, A:D.154 EDO.2: 5 residues within 4Å: Chain B: W.326, D.327, I.329, L.331 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.326 Water bridges: B:D.327 EDO.3: 7 residues within 4Å: Chain B: Q.292, D.293, L.294, N.295, G.375, Y.376, N.388 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.292, B:L.294, B:N.295, B:G.375 Water bridges: B:D.293, B:S.390, B:N.478 EDO.4: 5 residues within 4Å: Chain B: R.287, Q.288, R.291, I.329 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.287, B:Q.288, B:R.291 EDO.5: 5 residues within 4Å: Chain A: Q.37, D.38 Chain B: S.508, F.510, D.518 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.38, A:D.38 EDO.6: 6 residues within 4Å: Chain B: N.241, F.256, L.257, W.258, N.388, K.394 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.241, B:L.257, B:N.388, B:K.394 Water bridges: B:A.255, B:N.388 EDO.7: 7 residues within 4Å: Chain A: Y.197, F.201 Chain B: D.73, R.199, L.221, Y.248, P.249 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.197, A:Y.197, B:D.73, B:R.199, B:R.199 Water bridges: B:D.73 EDO.8: 9 residues within 4Å: Chain A: K.179, L.181 Chain B: D.73, P.205, R.206, P.249, A.250, S.251, D.252 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.73, A:K.179, A:K.179 EDO.9: 6 residues within 4Å: Chain B: R.291, E.475, Q.477, E.529, N.530, F.531 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.291, B:E.475, B:Q.477, B:N.530 EDO.10: 9 residues within 4Å: Chain A: S.195, Y.197, P.198 Chain B: E.224, M.225, N.226, P.227, K.228, Q.245 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.195, B:K.228, B:K.228, B:Q.245 EDO.11: 7 residues within 4Å: Chain A: R.145 Chain B: Q.23, F.24, G.25, G.385, S.386 Ligands: SOX.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.386, B:S.386

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 6 residues within 4Å: Chain A: E.152 Chain B: D.73, V.75, D.76, P.205, D.252 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:V.75, B:D.76, B:P.205, B:D.252, A:E.152

1 x SOX: N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-HYDROXY-3,3-DIMETHYL-7-OXO-4LAMBDA~4~-THIA-1-AZABICYCLO[3.2.0]HEPT-6-YL]-2-PHENYLAC ETAMIDE(Non-covalent)

SOX.13: 15 residues within 4Å: Chain A: M.142, F.146 Chain B: S.1, P.22, Q.23, F.24, S.67, T.68, A.69, F.71, N.241, R.263, S.386, N.388 Ligands: EDO.11 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.22, B:F.24, B:F.24, B:A.69, B:F.71, A:F.146 Hydrogen bonds: B:S.1, B:A.69, B:N.241, B:N.241 Salt bridges: B:R.263 pi-Stacking: A:F.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mcvey, C.E. et al., Crystal Structures of Penicillin Acylase Enzyme- Substrate Complexes: Structural Insights Into the Catalytic Mechanism. J.Mol.Biol. (2001)

Release Date

2001-11-28

Peptides

PENICILLIN G ACYLASE ALPHA SUBUNIT: A
PENICILLIN G ACYLASE BETA SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PENICILLIN G ACYLASE ALPHA SUBUNIT

PENICILLIN G ACYLASE BETA SUBUNIT

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