SMTL ID : 5nnp.1 (1 other biounit)

Structure of Naa15/Naa10 bound to HypK-THB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-oligomer

Ligands

1 x SER- GLU- SER- SER: Ser-Glu-Ser-Ser(Non-covalent)

SER-GLU-SER-SER.1: 11 residues within 4Å: Chain B: L.22, E.24, N.25, Y.26, Y.30, K.68, T.83, H.120, Y.147, Y.148 Ligands: CMC.18 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:E.24, B:E.24, B:N.25, B:Y.30, B:T.83, B:Y.147, B:Y.147, B:Y.147, B:Y.148 Water bridges: B:Y.26, B:H.120, B:H.120, B:Y.147 Salt bridges: B:K.68

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: E.189, D.220, Q.536, R.538, A.539, D.542 Chain B: P.39 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.536, A:R.538, A:A.539, A:D.542 Water bridges: A:I.537 GOL.3: 4 residues within 4Å: Chain A: K.419, K.450, R.454 Ligands: PO4.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.450, A:R.454, A:R.454 GOL.4: 6 residues within 4Å: Chain A: T.196, A.223, E.226, R.538 Ligands: GOL.2, GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.226, A:E.226, A:R.538 GOL.5: 6 residues within 4Å: Chain A: E.166, K.194, I.198, R.206, Q.209, H.210 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.166, A:K.194, A:R.206 Water bridges: A:E.173, A:K.194, A:D.214 GOL.6: 6 residues within 4Å: Chain A: E.163, E.166, H.167, T.170, R.201 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.163, A:E.166, A:H.167, A:T.170, A:R.201 GOL.7: 4 residues within 4Å: Chain A: E.163, K.164, H.167 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.163, A:K.164, A:K.164 Water bridges: A:E.163, A:E.163 GOL.8: 3 residues within 4Å: Chain A: K.311, T.315, E.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.315, A:E.352 GOL.9: 4 residues within 4Å: Chain A: H.411, K.414, T.430, Y.433 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.414 Water bridges: A:E.398, A:K.414 GOL.10: 6 residues within 4Å: Chain A: S.446, K.447, K.450, W.488 Chain B: H.16, E.20 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.16, A:S.446, A:K.447, A:K.450 GOL.11: 6 residues within 4Å: Chain A: R.549, E.552 Chain B: S.9, D.57, Y.58, P.59 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.9, A:R.549 Water bridges: B:S.9 GOL.12: 2 residues within 4Å: Chain A: R.549, Q.667 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.667, A:Q.667 GOL.13: 9 residues within 4Å: Chain A: H.157, Y.193, T.196, E.200, R.538, V.541, D.542, R.545 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.196, A:E.200, A:D.542, A:R.545 GOL.15: 8 residues within 4Å: Chain A: E.254, D.291, R.295, N.328 Chain B: M.1, I.3, L.94, K.99 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.291, A:R.295, A:N.328, B:K.99 Water bridges: A:E.254, A:R.295 GOL.16: 3 residues within 4Å: Chain C: D.7, A.9 Ligands: GOL.17 No protein-ligand interaction detected (PLIP) GOL.17: 3 residues within 4Å: Chain C: D.7, P.8 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.7

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.14: 6 residues within 4Å: Chain A: R.416, K.419, K.447, K.450, Y.451 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.416, A:K.419, A:K.447, A:K.450

1 x CMC: CARBOXYMETHYL COENZYME *A(Non-covalent)

CMC.18: 25 residues within 4Å: Chain A: R.289, K.320 Chain B: N.21, L.22, S.84, L.85, S.86, V.87, R.92, R.93, L.94, G.95, I.96, A.97, E.98, H.120, V.121, N.125, A.127, A.128, H.130, L.131, Y.132, T.135 Ligands: SER-GLU-SER-SER.1 25 PLIP interactions: 18 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.22, B:A.97, B:A.128 Hydrogen bonds: B:L.85, B:L.85, B:V.87, B:R.92, B:R.93, B:L.94, B:G.95, B:G.95, B:I.96, B:A.97, B:E.98, B:N.125, B:T.135 Water bridges: B:R.92, B:H.130, A:R.289, A:R.289, A:K.320, A:K.320, A:D.441 Salt bridges: A:R.289, A:K.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weyer, F.A. et al., Structural basis of HypK regulating N-terminal acetylation by the NatA complex. Nat Commun (2017)

Release Date

2017-06-14

Peptides

N-terminal acetyltransferase-like protein: A
Putative uncharacterized protein: B
Putative uncharacterized protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

N-terminal acetyltransferase-like protein

Putative uncharacterized protein

Putative uncharacterized protein

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