SMTL ID : 2evr.1

CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (NPUN_R0659) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.60 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 5 residues within 4Å: Chain A: D.39, S.40, C.43, T.44, R.45 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: D.39, S.40, C.43, T.44, R.45 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: E.111 Chain B: V.173, A.174, L.193, A.194 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.174, B:L.193 Water bridges: B:D.195 NA.9: 5 residues within 4Å: Chain A: V.173, A.174, L.193, A.194 Chain B: E.111 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.174, B:E.111 Water bridges: A:D.195

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

EDO.3: 6 residues within 4Å: Chain A: R.54, T.131, Q.143, A.144, A.147, W.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.143 Water bridges: A:R.54 EDO.4: 5 residues within 4Å: Chain A: N.124, R.208, D.209, G.210, I.211 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.124, A:N.124 Water bridges: A:N.124, A:N.124, A:R.208, A:I.211 EDO.5: 4 residues within 4Å: Chain A: D.34, L.35, N.36, D.84 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.36 Water bridges: A:N.36, A:N.36, A:D.84, A:D.84, A:D.84 EDO.6: 5 residues within 4Å: Chain A: Q.49, L.127, G.133, P.134, N.135 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.49, A:G.133, A:N.135, A:N.135 Water bridges: A:N.36, A:N.36, A:N.36 EDO.7: 4 residues within 4Å: Chain A: A.98, T.99, F.100, E.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.99 EDO.10: 6 residues within 4Å: Chain B: R.54, T.131, Q.143, A.144, A.147, W.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.143 Water bridges: B:R.54 EDO.11: 5 residues within 4Å: Chain B: N.124, R.208, D.209, G.210, I.211 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.124, B:N.124 Water bridges: B:N.124, B:N.124, B:R.208, B:I.211 EDO.12: 4 residues within 4Å: Chain B: D.34, L.35, N.36, D.84 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.36 Water bridges: B:N.36, B:N.36, B:D.84, B:D.84, B:D.84, B:D.84 EDO.13: 5 residues within 4Å: Chain B: Q.49, L.127, G.133, P.134, N.135 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.49, B:G.133, B:N.135, B:N.135 Water bridges: B:N.36, B:N.36, B:N.36 EDO.14: 4 residues within 4Å: Chain B: A.98, T.99, F.100, E.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Q. et al., Structural Basis of Murein Peptide Specificity of a gamma-D-Glutamyl-L-Diamino Acid Endopeptidase. Structure (2009)

Release Date

2005-11-22

Peptides

COG0791: Cell wall-associated hydrolases (invasion-associated proteins): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

COG0791: Cell wall-associated hydrolases (invasion-associated proteins)

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