SMTL ID : 4a1i.1 (4 other biounits)

ykud from B.subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: H.124, S.137, K.138, G.139, C.140, R.142 Chain B: H.120 Ligands: CD.5, CL.6 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.138, A:G.139, A:C.140 Water bridges: A:H.124 Salt bridges: A:H.124, A:R.142, B:H.120 SO4.2: 3 residues within 4Å: Chain A: T.93, R.165 Chain B: N.14 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.14 Water bridges: A:T.93, A:R.165, A:R.165, A:R.165 Salt bridges: A:R.165 SO4.3: 3 residues within 4Å: Chain A: N.128, V.136, R.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.128 Salt bridges: A:R.142 SO4.4: 1 residues within 4Å: Chain A: L.13 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.13, A:L.13, A:L.13 SO4.7: 9 residues within 4Å: Chain A: H.120 Chain B: H.124, S.137, K.138, G.139, C.140, R.142 Ligands: CD.10, CL.11 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.138, B:G.139, B:C.140 Water bridges: B:R.142, B:R.142 Salt bridges: B:H.124, B:R.142, A:H.120 SO4.8: 2 residues within 4Å: Chain B: Y.97, R.160 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.97, B:Y.97 Salt bridges: B:R.160 SO4.9: 2 residues within 4Å: Chain B: N.128, R.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.128 Salt bridges: B:R.142

2 x CD: CADMIUM ION(Non-covalent)

CD.5: 5 residues within 4Å: Chain A: H.120, C.140 Chain B: H.120 Ligands: SO4.1, CL.6 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:C.140, B:H.120, H2O.8 CD.10: 5 residues within 4Å: Chain A: H.120 Chain B: H.120, C.140 Ligands: SO4.7, CL.11 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:C.140, A:H.120, H2O.14

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

CL.6: 7 residues within 4Å: Chain A: F.109, W.113, H.120 Chain B: H.120, K.138 Ligands: SO4.1, CD.5 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain A: H.120, K.138 Chain B: F.109, W.113, H.120 Ligands: SO4.7, CD.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaise, M. et al., Structures of Three New Crystal Forms of the Ykud L,D-Transpeptidase from B. Subtilis. To be Published

Release Date

2012-09-26

Peptides

PUTATIVE L, D-TRANSPEPTIDASE YKUD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

PUTATIVE L, D-TRANSPEPTIDASE YKUD

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