SMTL ID : 4j9v.1

Crystal Structure of the TrkA Gating ring bound to ATP-gamma-S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-tetramer

Ligands

8 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 15 residues within 4Å: Chain A: G.7, A.8, G.9, Q.10, V.11, D.30, N.31, N.32, G.50, H.51, A.52, N.74, R.98, R.100, Q.351 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.8, A:A.8, A:Q.10, A:V.11, A:N.31, A:H.51, A:A.52, A:N.74, A:R.98, A:R.98, A:R.100, A:Q.351 Salt bridges: A:R.98, A:R.100 pi-Stacking: A:H.51 AGS.2: 11 residues within 4Å: Chain A: G.239, G.241, N.242, E.261, R.262, G.282, D.283, A.284, T.305, N.306, T.310 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.242, A:R.262, A:D.283, A:A.284, A:N.306, A:N.306 AGS.4: 18 residues within 4Å: Chain B: G.7, A.8, G.9, Q.10, V.11, D.30, N.31, N.32, R.35, G.50, H.51, A.52, V.72, T.73, N.74, R.98, R.100, Q.351 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:A.8, B:A.8, B:Q.10, B:V.11, B:N.31, B:N.31, B:N.32, B:H.51, B:A.52, B:N.74, B:R.98, B:R.98, B:R.100 Salt bridges: B:R.35, B:R.98, B:R.100 pi-Stacking: B:H.51 AGS.5: 17 residues within 4Å: Chain B: E.126, V.238, G.239, G.241, N.242, I.260, E.261, R.262, D.263, R.266, G.282, D.283, A.284, T.305, N.306, E.307, T.310 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.242, B:N.242, B:R.262, B:D.263, B:R.266, B:R.266, B:D.283, B:A.284 Salt bridges: B:R.266, B:R.266 AGS.8: 15 residues within 4Å: Chain C: G.7, A.8, G.9, Q.10, V.11, D.30, N.31, N.32, G.50, H.51, A.52, N.74, R.98, R.100, Q.351 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:A.8, C:A.8, C:Q.10, C:V.11, C:N.31, C:H.51, C:A.52, C:N.74, C:R.98, C:R.98, C:R.100, C:Q.351 Salt bridges: C:R.98, C:R.100 pi-Stacking: C:H.51 AGS.9: 11 residues within 4Å: Chain C: G.239, G.241, N.242, E.261, R.262, G.282, D.283, A.284, T.305, N.306, T.310 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.242, C:R.262, C:D.283, C:A.284, C:N.306, C:N.306 AGS.11: 18 residues within 4Å: Chain D: G.7, A.8, G.9, Q.10, V.11, D.30, N.31, N.32, R.35, G.50, H.51, A.52, V.72, T.73, N.74, R.98, R.100, Q.351 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:A.8, D:A.8, D:Q.10, D:V.11, D:N.31, D:N.31, D:N.32, D:H.51, D:A.52, D:N.74, D:R.98, D:R.98, D:R.100 Salt bridges: D:R.35, D:R.98, D:R.100 pi-Stacking: D:H.51 AGS.12: 17 residues within 4Å: Chain D: E.126, V.238, G.239, G.241, N.242, I.260, E.261, R.262, D.263, R.266, G.282, D.283, A.284, T.305, N.306, E.307, T.310 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.242, D:N.242, D:R.262, D:D.263, D:R.266, D:R.266, D:D.283, D:A.284, D:T.310 Salt bridges: D:R.266, D:R.266

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: Q.84, A.116 Chain B: Q.84, A.116 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:A.116, B:A.116 MG.7: 3 residues within 4Å: Chain B: R.175, H.423, D.424 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain C: Q.84, A.116 Chain D: Q.84, A.116 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:A.116, C:A.116 MG.14: 3 residues within 4Å: Chain D: R.175, H.423, D.424 No protein-ligand interaction detected (PLIP)

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

SO4.6: 1 residues within 4Å: Chain B: Q.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.138 SO4.13: 1 residues within 4Å: Chain D: Q.138 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., Gating of the TrkH ion channel by its associated RCK protein TrkA. Nature (2013)

Release Date

2013-04-10

Peptides

Potassium uptake protein TrkA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Potassium uptake protein TrkA

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