SMTL ID : 5txu.1

1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Apo Conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.134, C.140, H.145, C.146 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.134, A:C.140, A:H.145, A:C.146

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

NA.2: 3 residues within 4Å: Chain A: K.179, D.352, Y.354 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.179 NA.3: 2 residues within 4Å: Chain A: K.294, N.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.296

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

CL.4: 2 residues within 4Å: Chain A: E.101, Q.324 Ligand excluded by PLIP

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

FMT.5: 4 residues within 4Å: Chain A: Y.249, K.282, L.284, D.288 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: E.206, E.207, V.208, F.209 Ligand excluded by PLIP FMT.7: 6 residues within 4Å: Chain A: M.90, E.91, R.119, V.175, G.180, Y.354 Ligand excluded by PLIP FMT.8: 4 residues within 4Å: Chain A: A.248, Y.249, D.288, V.292 Ligand excluded by PLIP FMT.9: 4 residues within 4Å: Chain A: Y.249, S.250, T.251, K.282 Ligand excluded by PLIP FMT.10: 3 residues within 4Å: Chain A: Y.185, N.186, D.347 Ligand excluded by PLIP FMT.11: 5 residues within 4Å: Chain A: S.103, E.105, F.106, W.325, E.328 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: S.196, K.229, Y.316 Ligand excluded by PLIP FMT.13: 4 residues within 4Å: Chain A: K.201, S.218, V.219, E.220 Ligand excluded by PLIP FMT.14: 3 residues within 4Å: Chain A: I.81, T.141, Y.149 Ligand excluded by PLIP FMT.15: 2 residues within 4Å: Chain A: F.209, S.210 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain A: A.99, G.100, E.101, S.103 Ligands: FMT.20 Ligand excluded by PLIP FMT.17: 1 residues within 4Å: Chain A: K.170 Ligand excluded by PLIP FMT.18: 1 residues within 4Å: Chain A: F.209 Ligand excluded by PLIP FMT.19: 3 residues within 4Å: Chain A: K.229, N.296, Y.316 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain A: G.100, E.101 Ligands: FMT.16 Ligand excluded by PLIP

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.21: 4 residues within 4Å: Chain A: P.222, Y.223, Y.335, H.343 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.343 DMS.22: 12 residues within 4Å: Chain A: F.195, T.197, S.199, T.273, S.297, N.299, K.314, G.315, Y.316, G.317, H.318, G.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.316 Water bridges: A:S.199 DMS.23: 3 residues within 4Å: Chain A: S.260, F.304, G.305 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.238, A:N.238 Salt bridges: A:E.306 DMS.24: 5 residues within 4Å: Chain A: Y.121, P.192, L.193, Y.194, H.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.194 pi-Cation interactions: A:Y.194 DMS.25: 3 residues within 4Å: Chain A: E.333, G.334, Y.335 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocadello, S. et al., 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Apo Conformation. To Be Published

Release Date

2016-12-14

Peptides

Stage II sporulation protein D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Stage II sporulation protein D