SMTL ID : 6nci.1

Crystal structure of CDP-Chase: Vector data collection

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.91, L.178, S.179, I.180, A.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.180, A:A.181 Water bridges: A:K.91 Salt bridges: A:K.91 SO4.2: 4 residues within 4Å: Chain A: K.125, K.202 Chain B: E.201, K.202 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.202 Salt bridges: A:K.125, A:K.202 SO4.3: 1 residues within 4Å: Chain A: W.51 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.52 SO4.4: 2 residues within 4Å: Chain A: N.78, K.80 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.80 SO4.8: 3 residues within 4Å: Chain B: K.85, G.90, W.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.92 Water bridges: B:N.177, B:N.177 Salt bridges: B:K.85 SO4.9: 4 residues within 4Å: Chain A: W.8 Chain B: S.41, S.44, H.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.44 Salt bridges: B:H.45

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 3 residues within 4Å: Chain A: Y.22 Chain B: W.98 Ligands: RB5.7 No protein-ligand interaction detected (PLIP)

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

PEG.6: 3 residues within 4Å: Chain A: H.45 Chain B: K.4, W.8 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.4, A:H.45 Water bridges: A:H.45, A:K.48

1 x RB5: D-ribose(Non-covalent)

RB5.7: 5 residues within 4Å: Chain A: Y.22 Chain B: Y.27, R.31, W.98 Ligands: PO4.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.31 Water bridges: B:R.31, B:R.31, A:Y.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, M.S. et al., Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II. Molecules (2019)

Release Date

2019-02-06

Peptides

Phosphohydrolase (MutT/nudix family protein): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphohydrolase (MutT/nudix family protein)

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