SMTL ID : 2zgi.1

Crystal Structure of Putative 4-amino-4-deoxychorismate lyase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.44, R.47, H.48, R.124, E.181 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Water bridges: A:R.47, A:H.48, A:H.48, C:R.210, C:R.210, C:R.210, C:R.210 Salt bridges: A:R.47, A:H.48 SO4.4: 5 residues within 4Å: Chain B: R.44, R.47, H.48, R.124, E.181 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.181 Water bridges: B:R.47, B:R.124, B:R.124 Salt bridges: B:R.47, B:H.48 SO4.8: 5 residues within 4Å: Chain C: R.44, R.47, H.48, R.124, E.181 7 PLIP interactions: 7 interactions with chain C Water bridges: C:R.47, C:H.48, C:R.124, C:R.124, C:E.181 Salt bridges: C:R.47, C:H.48 SO4.11: 5 residues within 4Å: Chain D: R.44, R.47, H.48, R.124, E.181 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.181 Water bridges: D:R.124, D:E.181 Salt bridges: D:R.47, D:H.48

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.2: 16 residues within 4Å: Chain A: R.44, K.126, Y.130, Y.133, D.159, G.160, S.161, R.162, T.163, S.164, L.180, G.182, I.183, T.184, G.217, S.218 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.126, A:Y.133, A:L.180 Hydrogen bonds: A:K.126, A:S.161, A:I.183, A:T.184, A:T.184, A:S.218 Water bridges: A:K.126, A:S.164, A:G.182, A:S.218, A:G.219 Salt bridges: A:R.44, A:K.126 PLP.5: 17 residues within 4Å: Chain B: R.44, K.126, Y.130, Y.133, D.159, G.160, S.161, R.162, T.163, S.164, L.180, G.182, I.183, T.184, A.216, G.217, S.218 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.126, B:Y.133, B:L.180 Hydrogen bonds: B:I.183, B:T.184, B:S.218 Water bridges: B:K.126, B:R.162, B:S.164, B:L.180, B:S.218, B:S.218 Salt bridges: B:R.44, B:K.126 PLP.9: 16 residues within 4Å: Chain C: R.44, K.126, Y.130, Y.133, D.159, G.160, S.161, R.162, T.163, S.164, L.180, G.182, I.183, T.184, G.217, S.218 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:K.126, C:Y.133, C:L.180 Hydrogen bonds: C:I.183, C:T.184, C:T.184, C:S.218 Water bridges: C:T.26, C:T.26, C:T.27, C:K.126, C:K.126, C:S.164, C:L.180, C:G.182 Salt bridges: C:R.44, C:K.126 PLP.12: 16 residues within 4Å: Chain D: R.44, K.126, Y.130, Y.133, D.159, G.160, S.161, R.162, T.163, S.164, L.180, G.182, I.183, T.184, G.217, S.218 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:K.126, D:Y.133, D:L.180 Hydrogen bonds: D:S.161, D:I.183, D:T.184, D:S.218 Water bridges: D:R.44, D:R.44, D:R.162, D:S.164, D:L.180, D:G.219 Salt bridges: D:R.44, D:K.126

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 6 residues within 4Å: Chain A: R.169, Y.174, L.203, F.204, R.205, G.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.169 Water bridges: A:R.205 PGE.10: 5 residues within 4Å: Chain C: R.46, Y.56, G.58, D.59, E.60 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.46, C:D.59, C:E.60 Water bridges: C:A.61

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

PEG.6: 3 residues within 4Å: Chain B: L.203, F.204, G.208 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.169, B:R.169, B:R.205, B:R.205 PEG.7: 3 residues within 4Å: Chain B: R.201 Chain D: R.169, R.210 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.201, B:R.201 Water bridges: D:R.169, D:E.170, D:E.170 PEG.13: 2 residues within 4Å: Chain D: P.99, P.101 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Padmanabhan, B. et al., Structure of putative 4-amino-4-deoxychorismate lyase from Thermus thermophilus HB8. Acta Crystallogr.,Sect.F (2009)

Release Date

2008-07-22

Peptides

Putative 4-amino-4-deoxychorismate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative 4-amino-4-deoxychorismate lyase