SMTL ID : 3icw.1

Structure of a Circular Permutation on Lipase B from Candida Antartica with Bound Suicide Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: V.228, S.229, L.233 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.233 Hydrogen bonds: A:S.229, A:S.229 NAG.2: 3 residues within 4Å: Chain A: P.103, P.104, N.108 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.9 Hydrogen bonds: A:N.108 NAG.5: 3 residues within 4Å: Chain B: V.228, S.229, L.233 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.233 Hydrogen bonds: B:S.229, B:S.229 NAG.6: 3 residues within 4Å: Chain B: P.103, P.104, N.108 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.108 Water bridges: A:Q.9

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: K.242, R.283, S.284 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.284 Water bridges: A:R.283, A:A.285, A:A.285 Salt bridges: A:K.242, A:R.283 PO4.7: 3 residues within 4Å: Chain B: K.242, R.283, S.284 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.284 Water bridges: B:R.283, B:A.285, B:A.285 Salt bridges: B:K.242, B:R.283

2 x MHH: methyl hydrogen (R)-hexylphosphonate(Covalent)

MHH.4: 12 residues within 4Å: Chain A: G.73, T.74, W.138, S.139, Q.140, D.168, T.172, A.175, V.188, Q.191, I.223, H.258 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.172, A:A.175, A:V.188 Hydrogen bonds: A:T.74, A:T.74, A:Q.140 MHH.8: 12 residues within 4Å: Chain B: G.73, T.74, W.138, S.139, Q.140, D.168, T.172, A.175, V.188, Q.191, I.223, H.258 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.172, B:A.175, B:V.188 Hydrogen bonds: B:T.74, B:Q.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qian, Z. et al., Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation. J.Mol.Biol. (2009)

Release Date

2009-10-06

Peptides

Lipase B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lipase B

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