SMTL ID : 3ne8.1

The crystal structure of a domain from N-acetylmuramoyl-l-alanine amidase of Bartonella henselae str. Houston-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.13, E.28, H.82, D.84, E.115 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.13, A:E.28, A:H.82, A:D.84, A:E.115 ZN.9: 5 residues within 4Å: Chain B: H.13, E.28, H.82, D.84, E.115 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.13, B:E.28, B:H.82, B:D.84, B:E.115

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: S.162, A.214, S.215, Y.218 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.214 Hydrogen bonds: A:S.162 Water bridges: A:S.215 ACT.3: 4 residues within 4Å: Chain A: R.62, S.64, E.65, E.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.64, A:S.64 Salt bridges: A:R.62 ACT.4: 3 residues within 4Å: Chain A: R.6, I.50, F.73 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.6 ACT.10: 4 residues within 4Å: Chain B: S.162, A.214, S.215, Y.218 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.214 Hydrogen bonds: B:S.162 Water bridges: B:S.215 ACT.11: 4 residues within 4Å: Chain B: R.62, S.64, E.65, E.127 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.64, B:S.64 Water bridges: B:E.65, B:E.65, B:E.65 Salt bridges: B:R.62 ACT.12: 3 residues within 4Å: Chain B: R.6, I.50, F.73 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.6

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.5: 2 residues within 4Å: Chain A: E.42, A.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.42 FMT.13: 2 residues within 4Å: Chain B: E.42, A.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.42, B:E.42

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: I.99, R.141, T.144, H.145, L.179, K.180, A.181 Chain B: M.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.141, A:R.141 GOL.7: 5 residues within 4Å: Chain A: N.150, N.154, Q.222, F.223, Y.226 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.150, A:N.150 Water bridges: A:N.154, A:N.154, B:N.150 GOL.8: 7 residues within 4Å: Chain A: T.140, E.143, T.144, F.147, D.183, P.185 Chain B: R.142 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.142, A:E.143, A:T.144, A:T.144 Water bridges: B:R.142, A:D.183 GOL.14: 8 residues within 4Å: Chain A: M.231 Chain B: I.99, R.141, T.144, H.145, L.179, K.180, A.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.141, B:R.141 GOL.15: 5 residues within 4Å: Chain B: N.150, N.154, Q.222, F.223, Y.226 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.150, B:N.150 Water bridges: B:N.154, B:N.154, A:N.150 GOL.16: 7 residues within 4Å: Chain A: R.142 Chain B: T.140, E.143, T.144, F.147, D.183, P.185 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.144, A:R.142 Water bridges: B:D.183, A:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, D.C. et al., A conformational switch controls cell wall-remodelling enzymes required for bacterial cell division. Mol.Microbiol. (2012)

Release Date

2010-07-14

Peptides

N-acetylmuramoyl-l-alanine amidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-acetylmuramoyl-l-alanine amidase