SMTL ID : 4hvy.2 (1 other biounit)

A thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony Filtration

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: V.84, E.86 Chain C: L.81, L.82, S.83 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:E.86, C:L.82, C:V.84 Water bridges: C:T.80, C:L.81 GOL.10: 6 residues within 4Å: Chain A: L.136, H.137, E.140 Chain C: H.133, D.134 Ligands: GOL.30 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:H.133 Hydrogen bonds: A:H.137, A:E.140 GOL.11: 5 residues within 4Å: Chain B: V.84, E.86 Chain D: L.81, L.82, S.83 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:L.82, D:V.84, B:E.86 Water bridges: D:T.80, D:T.80 GOL.20: 6 residues within 4Å: Chain B: L.136, H.137, E.140 Chain D: H.133, D.134 Ligands: GOL.40 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.137, B:H.137, B:E.140 Water bridges: D:H.133 GOL.21: 5 residues within 4Å: Chain A: L.81, L.82, S.83 Chain C: V.84, E.86 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:L.82, A:V.84, C:E.86 Water bridges: A:T.80, A:L.81 GOL.30: 6 residues within 4Å: Chain A: H.133, D.134 Chain C: L.136, H.137, E.140 Ligands: GOL.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:H.133 Hydrogen bonds: C:H.137, C:E.140 GOL.31: 5 residues within 4Å: Chain B: L.81, L.82, S.83 Chain D: V.84, E.86 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:E.86, B:L.82, B:V.84 Water bridges: B:T.80, B:T.80 GOL.40: 6 residues within 4Å: Chain B: H.133, D.134 Chain D: L.136, H.137, E.140 Ligands: GOL.20 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:H.137, D:H.137, D:E.140 Water bridges: B:H.133

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: L.105, W.120 No protein-ligand interaction detected (PLIP) MG.3: 7 residues within 4Å: Chain A: A.24, V.25, F.26, V.33, L.34, L.49, P.50 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.24, A:L.34 MG.6: 5 residues within 4Å: Chain A: Q.148 Chain C: G.88, P.89, S.90, W.91 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: L.105, W.120 No protein-ligand interaction detected (PLIP) MG.13: 7 residues within 4Å: Chain B: A.24, V.25, F.26, V.33, L.34, L.49, P.50 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.24, B:L.34 MG.16: 5 residues within 4Å: Chain B: Q.148 Chain D: G.88, P.89, S.90, W.91 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain C: L.105, W.120 No protein-ligand interaction detected (PLIP) MG.23: 7 residues within 4Å: Chain C: A.24, V.25, F.26, V.33, L.34, L.49, P.50 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.24, C:L.34 MG.26: 5 residues within 4Å: Chain A: G.88, P.89, S.90, W.91 Chain C: Q.148 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain D: L.105, W.120 No protein-ligand interaction detected (PLIP) MG.33: 7 residues within 4Å: Chain D: A.24, V.25, F.26, V.33, L.34, L.49, P.50 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:A.24, D:L.34 MG.36: 5 residues within 4Å: Chain B: G.88, P.89, S.90, W.91 Chain D: Q.148 No protein-ligand interaction detected (PLIP)

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

SO4.4: 4 residues within 4Å: Chain A: T.128, P.129, L.130, H.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.128, A:L.130 Salt bridges: A:H.133 SO4.14: 4 residues within 4Å: Chain B: T.128, P.129, L.130, H.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.128, B:T.128, B:L.130 Salt bridges: B:H.133 SO4.24: 4 residues within 4Å: Chain C: T.128, P.129, L.130, H.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.128, C:L.130 Salt bridges: C:H.133 SO4.34: 4 residues within 4Å: Chain D: T.128, P.129, L.130, H.133 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.128, D:T.128, D:L.130 Salt bridges: D:H.133

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

NA.5: 3 residues within 4Å: Chain A: V.61, E.62, Q.65 Ligand excluded by PLIP NA.7: 2 residues within 4Å: Chain A: H.75, T.101 Ligand excluded by PLIP NA.8: 2 residues within 4Å: Chain A: A.132, H.133 Ligand excluded by PLIP NA.9: 1 residues within 4Å: Chain A: R.131 Ligand excluded by PLIP NA.15: 3 residues within 4Å: Chain B: V.61, E.62, Q.65 Ligand excluded by PLIP NA.17: 2 residues within 4Å: Chain B: H.75, T.101 Ligand excluded by PLIP NA.18: 2 residues within 4Å: Chain B: A.132, H.133 Ligand excluded by PLIP NA.19: 1 residues within 4Å: Chain B: R.131 Ligand excluded by PLIP NA.25: 3 residues within 4Å: Chain C: V.61, E.62, Q.65 Ligand excluded by PLIP NA.27: 2 residues within 4Å: Chain C: H.75, T.101 Ligand excluded by PLIP NA.28: 2 residues within 4Å: Chain C: A.132, H.133 Ligand excluded by PLIP NA.29: 1 residues within 4Å: Chain C: R.131 Ligand excluded by PLIP NA.35: 3 residues within 4Å: Chain D: V.61, E.62, Q.65 Ligand excluded by PLIP NA.37: 2 residues within 4Å: Chain D: H.75, T.101 Ligand excluded by PLIP NA.38: 2 residues within 4Å: Chain D: A.132, H.133 Ligand excluded by PLIP NA.39: 1 residues within 4Å: Chain D: R.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Asial, I. et al., Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell. Nat Commun (2013)

Release Date

2014-01-01

Peptides

Nucleoside diphosphate-linked moiety X motif 18: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Nucleoside diphosphate-linked moiety X motif 18

Related Entries With Identical Sequence