SMTL ID : 4fo0.2 (1 other biounit)

Human actin-related protein Arp8 in its ATP-bound state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: K.257 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: K.257 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: G.23, S.24, T.25, T.26, R.28, G.254, D.255, Q.256, K.257, G.280, S.281, Q.313, K.316, E.317, G.508, G.509, G.510, M.512, F.513, R.551 Ligands: MG.1 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:T.25, A:T.26, A:T.26, A:D.255, A:D.255, A:Q.256, A:K.257, A:K.257, A:Q.313, A:Q.313, A:K.316, A:E.317, A:G.509, A:G.510, A:M.512 Water bridges: A:P.22, A:P.22, A:R.28, A:R.28, A:R.28, A:R.28, A:K.257, A:K.257, A:K.257, A:R.551 Salt bridges: A:R.28, A:R.28, A:K.257 pi-Stacking: A:F.513 ATP.13: 21 residues within 4Å: Chain B: G.23, S.24, T.25, T.26, R.28, G.254, D.255, Q.256, K.257, G.280, S.281, Q.313, K.316, E.317, G.508, G.509, G.510, M.512, F.513, R.551 Ligands: MG.12 31 PLIP interactions: 31 interactions with chain B Hydrogen bonds: B:S.24, B:S.24, B:T.25, B:T.26, B:T.26, B:D.255, B:D.255, B:D.255, B:Q.256, B:K.257, B:K.257, B:Q.313, B:Q.313, B:K.316, B:G.509, B:G.510, B:M.512 Water bridges: B:P.22, B:P.22, B:R.28, B:R.28, B:R.28, B:R.28, B:K.257, B:K.257, B:K.257, B:R.551 Salt bridges: B:R.28, B:R.28, B:K.257 pi-Stacking: B:F.513

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Q.74, P.364, A.365, F.367, G.368, I.369, M.374, G.475, A.477 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: G.122, N.123, K.124, Y.142 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: Q.76, L.79, K.80, D.83 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: Y.298, E.300, C.301, Q.302, D.308 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: T.318, F.319, H.321, I.326, H.332, K.354 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: W.125, T.126, N.127, T.128, S.129, N.144, D.147 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: K.57, P.145, T.304, N.305, K.306, M.307 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: I.12, Q.13, S.14, A.562, C.563 Chain B: Q.13, C.563 Ligands: GOL.21 Ligand excluded by PLIP GOL.14: 9 residues within 4Å: Chain B: Q.74, P.364, A.365, F.367, G.368, I.369, M.374, G.475, A.477 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: G.122, N.123, K.124, Y.142 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: Q.76, L.79, K.80, D.83 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: Y.298, E.300, C.301, Q.302, D.308 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: T.318, F.319, H.321, I.326, H.332, K.354 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: W.125, T.126, N.127, T.128, S.129, N.144, D.147 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: K.57, P.145, T.304, N.305, K.306, M.307 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain A: Q.13, C.563 Chain B: I.12, Q.13, S.14, A.562, C.563 Ligands: GOL.10 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain A: M.548, D.549, L.552, K.556 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: M.548, D.549, L.552, K.556 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerhold, C.B. et al., Structure of Actin-related protein 8 and its contribution to nucleosome binding. Nucleic Acids Res. (2012)

Release Date

2012-09-26

Peptides

Actin-related protein 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Actin-related protein 8

Related Entries With Identical Sequence