SMTL ID : 4o8x.1

Zinc-bound Rpn11 in complex with Rpn8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: K.82, K.83, I.84, N.85, A.86, K.87 Ligands: EDO.14, EDO.18 Ligand excluded by PLIP EDO.2: 14 residues within 4Å: Chain A: Y.23, T.28, K.29, E.30, N.31, K.32, R.33, C.34, S.96, G.97, P.98, R.101, V.126, K.127 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: P.56, F.57, E.58, F.68, L.69, D.70 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: L.100, R.101, A.102, S.103, D.104, L.105, K.106, F.155 Ligands: EDO.16 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: L.39, N.51, S.52, F.53, C.81, I.84 Chain B: M.92 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: E.30, N.31, K.32, E.61 Ligands: EDO.10 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: L.20, D.21, E.24, R.25 Chain B: R.101, T.207, E.210 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: D.41, A.42, N.43, K.89, Q.116 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: E.79, M.80, K.83 Chain B: V.87, F.88, K.91 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: N.31, K.32, E.59, E.61, R.101 Ligands: EDO.6 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: K.127, Q.129 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: D.65, V.66, W.67, F.68 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: E.58, E.59, D.60, E.61, V.66, F.68 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: K.83 Chain B: P.73, Q.74 Ligands: EDO.1 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: E.109, K.112, N.118, P.119, A.140, I.141, E.142, K.153 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: L.100, Y.138, T.154, F.155, H.157 Ligands: EDO.4 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: H.6, A.42, N.43, S.44, S.45 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain A: I.84, N.85 Chain B: H.41, A.44, G.45, V.50, Q.74 Ligands: EDO.1 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: F.58, V.59, D.60, R.136 Ligand excluded by PLIP EDO.20: 10 residues within 4Å: Chain B: E.49, V.50, M.51, M.72, P.73, Q.74, S.75, G.78, V.79, A.83 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: L.53, V.84, Q.89, V.105, F.130, L.133 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: K.97, D.102 Ligands: EDO.27 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: C.117, V.152, V.153, I.154, D.155 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: E.166, A.167, I.170 Chain B: L.39, R.43, P.144, S.147 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: N.72, Y.73, N.76 Chain B: K.91, D.94, M.95, Q.98 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: C.117, W.118, L.119, F.157, Y.197, S.199 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: T.26 Chain B: K.97, Q.98, T.99, G.100 Ligands: EDO.22 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: E.26, I.160, R.195, Y.198 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: L.176, L.180 Chain B: M.215, L.217, H.218, K.219, Q.221 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: H.174 Chain B: V.152, I.154, I.202, D.203, Y.204 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: L.193, N.194, R.195, H.196 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.32: 4 residues within 4Å: Chain B: H.110, H.112, S.120, D.123 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.110, B:H.112, B:D.123, B:D.123, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Worden, E.J. et al., Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-01-22

Peptides

26S proteasome regulatory subunit RPN8: A
26S proteasome regulatory subunit RPN11: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

26S proteasome regulatory subunit RPN8

26S proteasome regulatory subunit RPN11

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