SMTL ID : 4jll.1 (1 other biounit)

Crystal Structure of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1 covalently bound with FP-alkyne, Northeast Structural Genomics Consortium (NESG) Target OR273

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x SEF: ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate(Covalent)

SEF.1: 17 residues within 4Å: Chain A: I.4, H.6, F.110, T.111, S.112, H.126, M.129, G.130, I.133, G.144, V.145, H.146, K.150, S.151, A.154, Y.155, A.158 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.4, A:F.110, A:H.126, A:I.133, A:K.150, A:A.154, A:Y.155, A:Y.155, A:A.158 Water bridges: A:H.126

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: V.33, T.111, W.116 Ligands: EDO.4 Ligand excluded by PLIP

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

EDO.3: 5 residues within 4Å: Chain A: D.10, G.32, V.33, A.36 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.4: 8 residues within 4Å: Chain A: V.33, T.111, S.112, W.113, G.114, A.115 Ligands: CL.2, EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.113, A:A.115 Water bridges: A:S.112 EDO.5: 6 residues within 4Å: Chain A: G.41, G.42, P.43, S.44, G.66, N.67 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.42, A:S.44, A:S.44 Water bridges: A:G.66, A:N.67 EDO.6: 6 residues within 4Å: Chain A: S.112, G.114, V.117, A.122, H.126, Y.155 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.112, A:Y.155 Water bridges: A:S.112 EDO.7: 10 residues within 4Å: Chain A: G.9, D.10, I.11, V.33, T.111, V.145, H.146, G.147 Ligands: EDO.3, EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.10, A:I.11, A:H.146

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain A: G.9, D.10, I.11, E.13, F.14, V.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.10 Water bridges: A:Q.8, A:Q.8

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain A: G.80, D.81, E.82, P.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.26 Water bridges: A:G.80, A:G.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajagopalan, S. et al., Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat.Chem.Biol. (2014)

Release Date

2013-04-10

Peptides

Evolved variant of computationally designed serine hydrolase OSH55.4_H1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Evolved variant of computationally designed serine hydrolase OSH55.4_H1

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