SMTL ID : 5j2z.2 (1 other biounit)

PRV UL37 N-terminal half (R2 mutant)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.83, E.86 Chain B: R.383, D.386, D.387 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.83, A:E.86, B:R.383, B:D.387, H2O.3 CA.2: 5 residues within 4Å: Chain A: D.83, D.85 Chain B: D.386, D.387 Ligands: ACT.40 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.386, B:D.387, A:D.83, A:D.85, H2O.3 CA.3: 5 residues within 4Å: Chain A: D.312, D.314 Ligands: CA.4, CL.16, CL.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.312, A:D.314, A:D.314 CA.4: 2 residues within 4Å: Chain A: D.314 Ligands: CA.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.314, H2O.2 CA.5: 1 residues within 4Å: Chain A: D.359 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.359, A:D.359 CA.6: 4 residues within 4Å: Chain A: H.82, D.179 Ligands: ACT.18, ACT.21 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.82, A:D.179 CA.7: 3 residues within 4Å: Chain A: R.182 Ligands: ACT.19, ACT.39 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain A: D.351 Chain B: E.93 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.351, B:E.93, H2O.1, H2O.3, H2O.5 CA.9: 4 residues within 4Å: Chain A: E.86 Chain B: H.382, R.383, D.386 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.382, B:D.386, A:E.86, H2O.5 CA.10: 1 residues within 4Å: Chain A: E.325 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.325 CA.22: 5 residues within 4Å: Chain A: R.383, D.386, D.387 Chain B: D.83, E.86 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.83, B:E.86, A:R.383, A:D.387, H2O.5 CA.23: 5 residues within 4Å: Chain A: D.386, D.387 Chain B: D.83, D.85 Ligands: ACT.19 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.85, A:D.386, A:D.387, H2O.1, ACT.19 CA.24: 5 residues within 4Å: Chain B: D.312, D.314 Ligands: CA.25, CL.37, CL.38 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.312, B:D.314, B:D.314 CA.25: 2 residues within 4Å: Chain B: D.314 Ligands: CA.24 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.314, H2O.5 CA.26: 1 residues within 4Å: Chain B: D.359 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.359, B:D.359 CA.27: 4 residues within 4Å: Chain B: H.82, D.179 Ligands: ACT.39, ACT.42 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.82, B:D.179 CA.28: 3 residues within 4Å: Chain B: R.182 Ligands: ACT.18, ACT.40 3 PLIP interactions: 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.3, H2O.3, ACT.18 CA.29: 2 residues within 4Å: Chain A: E.93 Chain B: D.351 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.93, B:D.351, H2O.2, H2O.4, H2O.5 CA.30: 4 residues within 4Å: Chain A: H.382, R.383, D.386 Chain B: E.86 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.86, A:H.382, A:D.386, H2O.3 CA.31: 1 residues within 4Å: Chain B: E.325 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.325

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

NA.11: 2 residues within 4Å: Chain A: D.403 Chain B: E.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.6 NA.12: 1 residues within 4Å: Chain A: Q.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.165, A:Q.165 NA.32: 2 residues within 4Å: Chain A: E.6 Chain B: D.403 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.403 NA.33: 1 residues within 4Å: Chain B: Q.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.165, B:Q.165

2 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.13: 10 residues within 4Å: Chain A: T.321, W.324, A.366, A.370, C.373, L.416, L.418, P.419, G.422, V.426 No protein-ligand interaction detected (PLIP) PE8.34: 10 residues within 4Å: Chain B: T.321, W.324, A.366, A.370, C.373, L.416, L.418, P.419, G.422, V.426 No protein-ligand interaction detected (PLIP)

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

PEG.14: 4 residues within 4Å: Chain A: W.84, D.85, R.142, Y.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.84 PEG.35: 4 residues within 4Å: Chain B: W.84, D.85, R.142, Y.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.84, B:Y.183

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

CL.15: 4 residues within 4Å: Chain A: D.179, R.182, Y.183 Ligands: ACT.18 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: D.312, L.313, D.314 Ligands: CA.3 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: D.312 Ligands: CA.3 Ligand excluded by PLIP CL.36: 4 residues within 4Å: Chain B: D.179, R.182, Y.183 Ligands: ACT.39 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain B: D.312, L.313, D.314 Ligands: CA.24 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain B: D.312 Ligands: CA.24 Ligand excluded by PLIP

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.18: 11 residues within 4Å: Chain A: H.82, D.83, W.84, D.85, D.179, Y.183 Chain B: Q.186 Ligands: CA.6, CL.15, CA.28, ACT.40 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.183 Hydrogen bonds: A:W.84 Salt bridges: B:R.182 ACT.19: 9 residues within 4Å: Chain A: R.182, Q.186, D.387, D.393 Chain B: D.83, D.85 Ligands: CA.7, CA.23, ACT.39 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.186 Water bridges: A:R.182, A:R.182, A:D.387 Salt bridges: A:R.182 ACT.20: 2 residues within 4Å: Chain A: R.363, T.365 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.363 Hydrogen bonds: A:R.363 Salt bridges: A:R.363 ACT.21: 6 residues within 4Å: Chain A: R.36, R.81, H.82, D.175, D.179 Ligands: CA.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.179 Hydrogen bonds: A:H.82, A:D.179 Salt bridges: A:R.36 ACT.39: 11 residues within 4Å: Chain A: Q.186 Chain B: H.82, D.83, W.84, D.85, D.179, Y.183 Ligands: CA.7, ACT.19, CA.27, CL.36 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.183 Hydrogen bonds: B:D.83, B:W.84 Salt bridges: A:R.182 ACT.40: 9 residues within 4Å: Chain A: D.83, D.85 Chain B: R.182, Q.186, D.387, D.393 Ligands: CA.2, ACT.18, CA.28 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.186 Water bridges: B:R.182, B:R.182, A:D.85 Salt bridges: B:R.182 ACT.41: 2 residues within 4Å: Chain B: R.363, T.365 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.363 Hydrogen bonds: B:R.363 Salt bridges: B:R.363 ACT.42: 6 residues within 4Å: Chain B: R.36, R.81, H.82, D.175, D.179 Ligands: CA.27 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.179 Hydrogen bonds: B:H.82 Salt bridges: B:R.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Richards, A.L. et al., The pUL37 tegument protein guides alpha-herpesvirus retrograde axonal transport to promote neuroinvasion. PLoS Pathog. (2017)

Release Date

2017-10-04

Peptides

UL37: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UL37

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