SMTL ID : 8rd3.1

Crystal structure of Saccharomyces cerevisiae Nmd4 protein bound to Upf1 helicase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: Y.426, L.427, F.430, P.431, M.465, L.582, L.589, H.610, F.611 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.429, A:F.430, A:L.582, A:H.610 Water bridges: A:E.429 EDO.3: 7 residues within 4Å: Chain A: K.150, K.156, D.346, T.347, K.348, K.371, G.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.150, A:K.156, A:D.346 EDO.4: 7 residues within 4Å: Chain A: S.185, I.186, F.189, A.190, L.192, V.221, T.225 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.186, A:T.225, A:K.254, A:K.254 EDO.5: 4 residues within 4Å: Chain A: V.451, Q.508, D.554, Y.555 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.508 EDO.6: 6 residues within 4Å: Chain A: K.235, D.236, R.237, N.328, A.330, D.331 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.331 EDO.8: 5 residues within 4Å: Chain A: G.216, Y.421, R.422, E.552, K.586 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.422, A:K.586, A:K.586 EDO.9: 5 residues within 4Å: Chain A: Q.191, Q.196, G.218, V.221, Y.421 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.191, A:N.193, A:Q.196 EDO.11: 3 residues within 4Å: Chain A: S.244, N.245, V.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.245, A:N.245, A:V.246 EDO.12: 8 residues within 4Å: Chain A: S.159, G.160, Y.161, I.174 Chain B: F.181, M.185, T.208, V.209 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.160, A:Y.161, B:V.209, B:V.209

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 10 residues within 4Å: Chain A: P.214, P.215, G.216, T.217, G.218, K.219, Q.384, R.422, G.550, R.584 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.216, A:T.217, A:G.218, A:K.219, A:Q.384, A:Q.384 Salt bridges: A:K.219, A:R.422, A:R.584

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 7 residues within 4Å: Chain A: Q.359, Q.384, L.385, Q.549, G.550, V.580, R.584 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.385, A:Q.549, A:G.550

1 x MLA: MALONIC ACID(Non-covalent)

MLA.10: 8 residues within 4Å: Chain A: I.512, P.514, V.545, F.571, L.572, D.574, R.577, L.578 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.514, A:R.577

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barbarin-Bocahu, I. et al., Structure of a yeast protein complex. To Be Published

Release Date

2024-08-14

Peptides

ATP-dependent helicase NAM7: A
Nonsense-mediated decay protein 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent helicase NAM7

Nonsense-mediated decay protein 4