SMTL ID : 3peg.2 (1 other biounit)

Crystal structure of Neurofibromins Sec14-PH module containing a patient derived duplication (TD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.50, R.51, P.180, A.182, T.183 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.180, A:A.182, A:T.183 Salt bridges: A:R.50, A:R.51 SO4.2: 3 residues within 4Å: Chain A: R.126, T.223, K.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.224 Salt bridges: A:R.126, A:K.130 SO4.3: 3 residues within 4Å: Chain A: R.92, K.94, T.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.95, A:T.95 Salt bridges: A:R.92, A:K.94 SO4.4: 3 residues within 4Å: Chain A: R.126, A.200, H.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.201 Salt bridges: A:R.126 SO4.5: 3 residues within 4Å: Chain A: S.142, K.143, R.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.143 Salt bridges: A:R.144 SO4.8: 5 residues within 4Å: Chain B: R.50, R.51, P.180, A.182, T.183 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.180, B:A.182, B:T.183 Salt bridges: B:R.50, B:R.51 SO4.9: 3 residues within 4Å: Chain B: R.126, T.223, K.224 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.223, B:K.224 Salt bridges: B:R.126, B:K.130 SO4.10: 3 residues within 4Å: Chain B: R.92, K.94, T.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.95 Salt bridges: B:R.92, B:K.94 SO4.11: 3 residues within 4Å: Chain B: R.126, A.200, H.201 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.201 Salt bridges: B:R.126 SO4.12: 3 residues within 4Å: Chain B: S.142, K.143, R.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.143 Salt bridges: B:R.144

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: P.89, S.90, N.258 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: P.89, S.90, N.258 No protein-ligand interaction detected (PLIP)

2 x PEV: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PEV.7: 19 residues within 4Å: Chain A: F.32, Y.47, Y.78, I.80, N.91, F.93, W.101, F.102, F.105, Y.110, V.113, V.116, I.118, Y.128, G.138, L.139, R.144 Chain B: R.134, T.137 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.32, A:Y.47, A:I.80, A:F.93, A:F.93, A:W.101, A:W.101, A:F.102, A:F.105, A:F.105, A:Y.110, A:V.113, A:V.116, A:I.118, A:Y.128, A:L.139 Water bridges: A:G.138 Hydrogen bonds: B:T.137 PEV.14: 19 residues within 4Å: Chain A: R.134, T.137 Chain B: F.32, Y.47, Y.78, I.80, N.91, F.93, W.101, F.102, F.105, Y.110, V.113, V.116, I.118, Y.128, G.138, L.139, R.144 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.32, B:Y.47, B:I.80, B:F.93, B:F.93, B:W.101, B:W.101, B:F.102, B:F.105, B:F.105, B:Y.110, B:V.113, B:V.116, B:I.118, B:Y.128, B:L.139 Water bridges: B:G.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Welti, S. et al., Structural and biochemical consequences of NF1 associated nontruncating mutations in the Sec14-PH module of neurofibromin. Hum.Mutat. (2011)

Release Date

2010-12-08

Peptides

Neurofibromin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Neurofibromin

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