SMTL ID : 4xnf.1

Tailspike protein double mutant D339A/E372Q of E. coli bacteriophage HK620

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-trimer

Ligands

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 3 residues within 4Å: Chain A: V.458, N.459, Y.487 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.459 Water bridges: B:E.469 TRS.9: 3 residues within 4Å: Chain B: V.458, N.459, Y.487 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:E.469 Hydrogen bonds: B:N.459 TRS.17: 3 residues within 4Å: Chain C: V.458, N.459, Y.487 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.459 Water bridges: A:E.469

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

FMT.2: 4 residues within 4Å: Chain A: N.558, L.559, D.560 Ligands: FMT.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.559, A:D.560 FMT.3: 6 residues within 4Å: Chain A: V.524, N.525, S.539, T.540, D.541, Y.544 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.523, A:N.525, A:N.525, A:T.540, A:D.541 FMT.4: 4 residues within 4Å: Chain A: R.30, D.34 Chain B: W.43, V.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.30 FMT.5: 6 residues within 4Å: Chain A: K.432, S.433, N.434, V.435, Q.465 Chain C: D.431 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:I.436, C:S.433 Hydrogen bonds: C:D.431, C:D.431 FMT.6: 4 residues within 4Å: Chain A: A.571 Chain B: E.557, L.559 Ligands: FMT.10 No protein-ligand interaction detected (PLIP) FMT.10: 4 residues within 4Å: Chain B: N.558, L.559, D.560 Ligands: FMT.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.559, B:D.560 FMT.11: 6 residues within 4Å: Chain B: V.524, N.525, S.539, T.540, D.541, Y.544 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.523, B:N.525, B:N.525, B:T.540, B:D.541 FMT.12: 4 residues within 4Å: Chain B: R.30, D.34 Chain C: W.43, V.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.30 FMT.13: 6 residues within 4Å: Chain A: D.431 Chain B: K.432, S.433, N.434, V.435, Q.465 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.431, A:D.431 Water bridges: A:S.433, B:I.436 FMT.14: 4 residues within 4Å: Chain B: A.571 Chain C: E.557, L.559 Ligands: FMT.18 No protein-ligand interaction detected (PLIP) FMT.18: 4 residues within 4Å: Chain C: N.558, L.559, D.560 Ligands: FMT.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.559, C:D.560 FMT.19: 6 residues within 4Å: Chain C: V.524, N.525, S.539, T.540, D.541, Y.544 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.523, C:N.525, C:N.525, C:T.540, C:D.541 FMT.20: 4 residues within 4Å: Chain A: W.43, V.53 Chain C: R.30, D.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.30 FMT.21: 6 residues within 4Å: Chain B: D.431 Chain C: K.432, S.433, N.434, V.435, Q.465 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.431, B:D.431 Water bridges: B:S.433, C:I.436 FMT.22: 4 residues within 4Å: Chain A: E.557, L.559 Chain C: A.571 Ligands: FMT.2 No protein-ligand interaction detected (PLIP)

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

NA.7: 3 residues within 4Å: Chain A: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.484, A:Q.484 NA.8: 4 residues within 4Å: Chain A: N.407 Chain C: R.372, V.373, T.402 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:V.373, C:T.402, A:N.407 Water bridges: C:C.401 NA.15: 3 residues within 4Å: Chain B: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.484, B:Q.484 NA.16: 4 residues within 4Å: Chain A: R.372, V.373, T.402 Chain B: N.407 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.373, A:T.402, B:N.407 Water bridges: A:C.401 NA.23: 3 residues within 4Å: Chain C: A.455, S.482, Q.484 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.455, C:Q.484 NA.24: 4 residues within 4Å: Chain B: R.372, V.373, T.402 Chain C: N.407 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.402, B:T.402, C:N.407 Water bridges: B:C.401

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Gohlke, U. et al., Enthalpic cost of water removal from a hydrophobic glucose binding cavity on HK620 tailspike protein. to be published

Release Date

2016-01-27

Peptides

Tail spike protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Tail spike protein