SMTL ID : 7rcz.1

Crystal structure of C. difficile SpoVD in complex with ampicillin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: K.193, K.197 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.193, A:K.197 SO4.2: 5 residues within 4Å: Chain A: K.205, K.206, Y.240, Q.259, R.262 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.259 Water bridges: A:K.206 Salt bridges: A:K.205, A:K.206, A:R.262 SO4.7: 1 residues within 4Å: Chain A: T.303 No protein-ligand interaction detected (PLIP) SO4.10: 2 residues within 4Å: Chain B: S.442, K.443 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.443, B:E.444 Salt bridges: B:K.443 SO4.11: 4 residues within 4Å: Chain B: K.206, Y.240, Q.259, R.262 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.240, B:Q.259 Water bridges: B:K.206 Salt bridges: B:K.205, B:K.206, B:R.262 SO4.12: 3 residues within 4Å: Chain B: K.21, V.37, T.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.38 Salt bridges: B:K.21 SO4.13: 6 residues within 4Å: Chain B: Q.140, Y.141, D.142, K.143, K.144 Ligands: SO4.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.143, B:K.144 Salt bridges: B:K.144 SO4.14: 3 residues within 4Å: Chain B: K.143, K.144 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.143, B:K.144 SO4.15: 3 residues within 4Å: Chain A: N.424, K.425 Chain B: R.313 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.313 SO4.16: 3 residues within 4Å: Chain B: T.458, K.463, Y.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.458 Water bridges: B:K.463 Salt bridges: B:K.463

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 7 residues within 4Å: Chain A: Q.196, Y.199, E.200, I.237, Y.238, P.239, Y.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.199, A:Y.240 EPE.6: 8 residues within 4Å: Chain A: Q.140, Y.141, D.142, K.143, K.144, G.361, I.362, D.363 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.140, A:K.143, A:K.144, A:I.362 Water bridges: A:D.142

1 x POL: N-PROPANOL(Non-covalent)

POL.4: 3 residues within 4Å: Chain A: F.296, T.297, E.337 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.337 Hydrogen bonds: A:T.297 Water bridges: A:E.294

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

PEG.5: 6 residues within 4Å: Chain A: D.504, Q.506, G.543, V.544, K.545 Chain B: T.517 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.506, A:K.545

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: C.298, C.311, H.318, C.331 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.298, A:C.311, A:H.318, A:C.331 ZN.17: 4 residues within 4Å: Chain B: C.298, C.311, H.318, C.331 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.298, B:C.311, B:H.318, B:C.331

2 x ZZ7: (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid(Covalent)

ZZ7.9: 12 residues within 4Å: Chain A: G.273, S.274, K.277, W.312, S.330, N.332, K.475, T.476, G.477, T.478, F.522, G.523 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.312, A:F.522, A:F.522 Hydrogen bonds: A:S.274, A:S.330, A:S.330, A:N.332, A:T.476, A:T.478, A:T.478, A:T.478, A:G.523 Salt bridges: A:K.475 ZZ7.18: 11 residues within 4Å: Chain B: G.273, S.274, W.312, S.330, Q.390, K.475, T.476, G.477, T.478, F.522, G.523 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.312, B:T.478, B:F.522, B:F.522 Hydrogen bonds: B:S.274, B:S.330, B:N.332, B:Q.390, B:T.476, B:T.478, B:T.478, B:T.478, B:G.523 Salt bridges: B:K.475

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sacco, M.D. et al., A unique class of Zn 2+ -binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. Nat Commun (2022)

Release Date

2022-03-23

Peptides

Stage V sporulation protein D (Sporulation specific penicillin-binding protein): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Stage V sporulation protein D (Sporulation specific penicillin-binding protein)