SMTL ID : 8itv.1

KL2.1 in complex with CRM1-Ran-RanBP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.24, T.42 Ligands: GTP.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.42, H2O.1, H2O.1

14 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 3 residues within 4Å: Chain A: V.137, R.140 Chain C: M.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.140 NO3.4: 5 residues within 4Å: Chain A: R.76, N.103, W.104, R.106, D.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.76, A:N.103, A:R.106, A:D.107 Water bridges: A:W.104 NO3.6: 8 residues within 4Å: Chain A: R.29, F.35, K.37, K.152, D.211, D.214 Chain B: K.31, E.44 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.31, B:E.44, B:E.44, A:R.29, A:R.29, A:K.37 NO3.9: 6 residues within 4Å: Chain A: A.133, I.136, H.139, Y.146 Chain C: E.360, K.363 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.360 NO3.11: 4 residues within 4Å: Chain C: T.323, T.364, D.367, Y.368 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.323, C:T.323, C:T.364 NO3.13: 2 residues within 4Å: Chain C: S.446, W.447 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.447 Water bridges: C:W.445, C:H.448, C:N.492 NO3.16: 7 residues within 4Å: Chain C: L.326, A.327, R.328, N.329, R.330, A.331 Ligands: ACT.30 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.331 Water bridges: C:R.328 NO3.17: 6 residues within 4Å: Chain C: R.80, K.81, H.950, K.985, E.986, V.987 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.950 Water bridges: C:R.80, C:K.81 NO3.18: 2 residues within 4Å: Chain C: E.388, Q.392 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.388 NO3.19: 4 residues within 4Å: Chain C: L.286, Q.287, A.290, N.345 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.286, C:N.345 NO3.20: 4 residues within 4Å: Chain C: R.403, E.405, W.455, Y.502 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.403, C:E.405 NO3.25: 4 residues within 4Å: Chain C: K.591, A.653, T.656, K.713 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.591, C:T.656, C:K.713, C:K.713 Water bridges: C:H.587, C:K.591, C:A.653 NO3.27: 3 residues within 4Å: Chain C: E.415, V.418, Y.419 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.419 NO3.28: 4 residues within 4Å: Chain C: F.170, K.186, N.187, S.190 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.190, C:S.190

9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 2 residues within 4Å: Chain A: V.9, K.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.9 DMS.7: 8 residues within 4Å: Chain A: H.139, R.140, N.143, L.144, Q.145 Chain C: Q.316, E.360, L.361 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.316, C:Q.316 DMS.15: 2 residues within 4Å: Chain C: N.791, D.832 No protein-ligand interaction detected (PLIP) DMS.21: 3 residues within 4Å: Chain C: D.55, I.93, F.96 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.55 Salt bridges: C:D.55 pi-Cation interactions: C:F.96 DMS.24: 6 residues within 4Å: Chain C: W.447, A.494, V.495, R.498, H.533, E.534 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:D.491, C:E.534 DMS.26: 5 residues within 4Å: Chain C: S.208, S.210, I.213, S.248, D.250 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.248 Salt bridges: C:D.250 DMS.29: 7 residues within 4Å: Chain C: K.490, K.493, A.494, F.528, E.531, H.533 Ligands: Q73.32 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:E.531 DMS.31: 5 residues within 4Å: Chain C: E.194, R.230, Y.231, E.234, T.235 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.230 Salt bridges: C:E.194, C:E.234 DMS.33: 6 residues within 4Å: Chain C: R.94, N.136, W.137, P.138, E.139, E.143 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.139 Salt bridges: C:E.143

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: D.125, S.153, Y.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.153, A:S.153 GOL.12: 6 residues within 4Å: Chain C: I.356, E.357, E.358, R.359, F.362, N.400 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.356, C:E.358, C:R.359, C:N.400 GOL.14: 5 residues within 4Å: Chain C: V.586, H.587, P.617, N.646, T.650 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.587 Water bridges: C:Y.590, C:Y.590 GOL.22: 6 residues within 4Å: Chain C: V.98, F.140, E.143, L.144, S.147, N.158 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.147, C:N.158 Water bridges: C:N.158 GOL.23: 3 residues within 4Å: Chain C: A.620, T.623, I.643 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.623, C:T.623

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.8: 27 residues within 4Å: Chain A: D.18, G.19, G.20, T.21, G.22, K.23, T.24, T.25, F.35, E.36, K.37, K.38, Y.39, V.40, A.41, T.42, A.67, G.68, L.69, N.122, K.123, D.125, I.126, S.150, A.151, K.152 Ligands: MG.1 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:G.22, A:K.23, A:T.24, A:T.24, A:T.25, A:T.25, A:E.36, A:Y.39, A:T.42, A:T.66, A:G.68, A:N.122, A:K.123, A:K.123, A:S.150, A:A.151, A:K.152 Water bridges: A:T.24, A:T.42, A:T.42, A:L.69, A:L.69, A:K.152 Salt bridges: A:K.23, A:K.23, A:D.125 pi-Stacking: A:F.35, A:F.35

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

CL.10: 2 residues within 4Å: Chain C: K.512, H.554 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.30: 4 residues within 4Å: Chain C: R.330, E.334, D.375 Ligands: NO3.16 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.375 Salt bridges: C:R.330, C:K.382

1 x Q73: (3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoic acid(Non-covalent)

Q73.32: 17 residues within 4Å: Chain C: V.474, I.477, K.478, L.481, C.484, E.485, K.493, A.497, I.500, M.501, F.510, H.514, F.517, T.520, K.524, F.528 Ligands: DMS.29 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:V.474, C:V.474, C:A.497, C:I.500, C:F.510, C:F.517, C:F.517, C:F.517, C:T.520, C:K.524, C:F.528 Hydrogen bonds: C:K.478, C:E.485, C:E.485 Salt bridges: C:K.493, C:K.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., KL2.1 in complex with CRM1-Ran-RanBP1. To Be Published

Release Date

2024-03-27

Peptides

GTP-binding nuclear protein Ran: A
YRB1 isoform 1: B
CRM1 isoform 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTP-binding nuclear protein Ran

YRB1 isoform 1

CRM1 isoform 1

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