SMTL ID : 7nw1.1 (1 other biounit)

Crystal structure of UFC1 in complex with UBA5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: T.93, T.94, A.95, K.123, W.126, A.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.95, A:A.127 Water bridges: A:A.95 EDO.2: 5 residues within 4Å: Chain A: D.104, G.105, T.107, M.110, Y.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.105, A:T.107 EDO.4: 6 residues within 4Å: Chain A: N.20, I.89, T.90, Y.91, P.92, T.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:T.93, A:T.93 EDO.7: 3 residues within 4Å: Chain A: R.26, E.27, V.30 No protein-ligand interaction detected (PLIP) EDO.8: 8 residues within 4Å: Chain A: R.32, P.92, W.126, N.129, V.130, P.131, K.132, F.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.32, A:P.92, A:N.129, A:N.129, A:F.133 EDO.14: 3 residues within 4Å: Chain A: R.24, D.25 Ligands: PEG.5 No protein-ligand interaction detected (PLIP) EDO.15: 7 residues within 4Å: Chain A: K.109, C.117, L.118, T.119, W.146, V.149, E.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.119, A:E.150 EDO.16: 3 residues within 4Å: Chain A: D.53, W.71, K.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.78 EDO.17: 3 residues within 4Å: Chain A: K.48, N.49, D.51 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 2 residues within 4Å: Chain A: E.97, K.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.115 PEG.5: 4 residues within 4Å: Chain A: D.25, E.27, L.28 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.27

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 10 residues within 4Å: Chain A: V.10, Y.43, N.52, W.54, W.71, Y.72, A.140, G.144, L.147 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.47, A:W.71

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: R.56, E.58, F.67, G.68, K.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.58 Water bridges: A:G.68 GOL.10: 5 residues within 4Å: Chain A: E.84, F.85, D.86, E.97, K.115 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.84, A:E.84, A:D.86, A:E.97, A:K.115, A:K.115 GOL.11: 7 residues within 4Å: Chain A: Y.79, L.154, I.155, G.158, V.159, I.160, H.162 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.79, A:I.155, A:G.158, A:I.160, A:H.162 GOL.12: 9 residues within 4Å: Chain A: E.80, F.81, E.102, L.103, K.106, V.159, I.160, Q.161, K.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.102, A:V.159, A:Q.161, A:Q.161, A:K.163 GOL.13: 3 residues within 4Å: Chain A: Y.72, I.73 Ligands: PGE.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.72, A:I.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, M. et al., Structural basis for UFM1 transfer from UBA5 to UFC1. Nat Commun (2021)

Release Date

2021-09-29

Peptides

Ubiquitin-fold modifier-conjugating enzyme 1: A
Ubiquitin-like modifier-activating enzyme 5: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
FFF

Ubiquitin-fold modifier-conjugating enzyme 1

Ubiquitin-like modifier-activating enzyme 5

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