SMTL ID : 6qa2.1

R80A MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.86, T.92, R.104, H.117 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.92 Water bridges: A:R.104, A:R.104, A:N.114 Salt bridges: A:R.86, A:R.104, A:H.117 SO4.2: 1 residues within 4Å: Chain A: R.86 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.86 SO4.3: 4 residues within 4Å: Chain B: R.86, T.92, R.104, H.117 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.86, B:G.90, B:R.104, B:R.104 Salt bridges: B:R.86, B:R.104, B:H.117 SO4.4: 1 residues within 4Å: Chain B: R.86 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.86, B:R.86 Salt bridges: B:R.86 SO4.6: 4 residues within 4Å: Chain C: R.86, T.92, R.104, H.117 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.104, C:R.104 Salt bridges: C:R.86, C:R.104, C:H.117 SO4.7: 1 residues within 4Å: Chain C: R.86 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.86 Salt bridges: C:R.86 SO4.9: 5 residues within 4Å: Chain D: R.86, T.92, R.104, H.117, G.118 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.118 Water bridges: D:K.10, D:R.104 Salt bridges: D:R.86, D:R.104, D:H.117 SO4.10: 1 residues within 4Å: Chain D: R.86 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.86, D:R.86 Salt bridges: D:R.86 SO4.11: 5 residues within 4Å: Chain E: R.86, T.92, R.104, H.117, G.118 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:T.92, E:G.118 Water bridges: E:K.10, E:R.104, E:R.104, E:R.104 Salt bridges: E:R.86, E:R.104, E:H.117 SO4.12: 2 residues within 4Å: Chain E: R.86, D.120 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.86, E:G.90 Salt bridges: E:R.86 SO4.13: 4 residues within 4Å: Chain F: R.86, T.92, R.104, H.117 5 PLIP interactions: 5 interactions with chain F Water bridges: F:R.104, F:R.104 Salt bridges: F:R.86, F:R.104, F:H.117 SO4.14: 1 residues within 4Å: Chain F: R.86 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.86

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.5: 9 residues within 4Å: Chain B: E.21, R.25, R.28 Chain D: E.21, R.25, R.28 Chain F: E.21, R.25, R.28 13 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D, 4 interactions with chain F Hydrogen bonds: B:E.21, B:E.21, B:R.25, B:R.28, B:R.28, D:E.21, D:R.25, D:R.28, D:R.28, F:E.21, F:R.25, F:R.28, F:R.28 TAM.8: 9 residues within 4Å: Chain A: E.21, R.25, R.28 Chain C: E.21, R.25, R.28 Chain E: E.21, R.25, R.28 9 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E, 4 interactions with chain C Hydrogen bonds: A:E.21, A:R.25, A:R.28, E:E.21, E:R.25, C:E.21, C:R.25, C:R.28, C:R.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dautant, A. et al., Remodeling of the Binding Site of Nucleoside Diphosphate Kinase Revealed by X-ray Structure and H/D Exchange. Biochemistry (2019)

Release Date

2019-02-27

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase