SMTL ID : 5jyb.1

Crystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.41, R.42, V.149 9 PLIP interactions: 9 interactions with chain A Water bridges: A:Q.38, A:Q.38, A:K.41, A:K.41, A:K.41, A:E.45, A:V.149 Salt bridges: A:K.41, A:R.42 SO4.7: 4 residues within 4Å: Chain B: Q.38, K.41, R.42, V.149 7 PLIP interactions: 7 interactions with chain B Water bridges: B:Q.38, B:R.42, B:V.149, B:V.149, B:V.149 Salt bridges: B:K.41, B:R.42 SO4.8: 2 residues within 4Å: Chain B: R.83 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.83

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.2: 8 residues within 4Å: Chain A: V.46, F.47, V.156, E.157, N.160, R.161, S.165, E.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.160 Water bridges: A:S.165 P6G.9: 9 residues within 4Å: Chain B: P.13, V.46, F.47, V.156, E.157, N.160, R.161, F.164, S.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.160 Water bridges: B:E.157

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

EPE.3: 9 residues within 4Å: Chain A: W.24, S.61, E.62, Y.65, Q.94, D.95 Chain B: K.258, R.262, Q.296 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B pi-Cation interactions: A:Y.65 Hydrogen bonds: B:Q.296, B:Q.296 Water bridges: B:K.258 Salt bridges: B:K.258, B:R.262 EPE.10: 6 residues within 4Å: Chain A: K.258, R.262, Q.296 Chain B: Y.65, Q.94, D.95 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Water bridges: B:Q.94, B:D.95, B:D.95, A:K.258, A:K.258 Hydrogen bonds: A:Q.296 Salt bridges: A:K.258, A:R.262

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 10 residues within 4Å: Chain A: I.16, T.50, V.52, P.53, M.54, P.55, T.77, D.81, R.83, V.84 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.83

2 x SBT: 2-BUTANOL(Non-covalent)

SBT.5: 10 residues within 4Å: Chain A: I.91, G.92, G.93, Y.118, A.119, D.120, T.143, W.185, S.248, E.249 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.119, A:T.143 Hydrogen bonds: A:G.92 Water bridges: A:D.120 SBT.13: 11 residues within 4Å: Chain A: Y.259 Chain B: G.93, Q.94, A.119, D.120, C.219, E.221, V.222, F.225, S.248, D.250 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.221, B:V.222, B:F.225, A:Y.259 Hydrogen bonds: B:D.250, B:D.250

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: W.232, P.233, K.235, W.238, Q.267, G.268, I.269, K.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.232, A:Q.267, A:K.272 GOL.14: 2 residues within 4Å: Chain B: E.234, K.235 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.235 Water bridges: B:P.233, B:P.233, B:E.234, B:K.236

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

EDO.11: 7 residues within 4Å: Chain B: I.16, V.52, M.54, D.81, R.83, V.84 Ligands: SO4.8 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: W.24, I.91, G.92, G.93 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases. To Be Published

Release Date

2016-06-15

Peptides

MccC family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MccC family protein