- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.76 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x GLY- GLY- ALA- ILE- SER: 5-mer lipopeptide from Protein Nef(Non-covalent)
- 5 x ZN: ZINC ION(Non-covalent)
ZN.2: 3 residues within 4Å:- Chain A: H.192, A.200, E.255
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:H.192, A:E.255
ZN.3: 2 residues within 4Å:- Chain A: H.193
- Chain B: D.99
3 PLIP interactions:1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: B:D.99, A:H.193, H2O.9
ZN.4: 3 residues within 4Å:- Chain A: A.1, H.4, Q.181
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:A.1, A:H.4
ZN.14: 2 residues within 4Å:- Chain B: H.52
- Ligands: EDO.21
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:H.52, H2O.9
ZN.15: 2 residues within 4Å:- Chain B: E.37
- Ligands: EDO.22
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.37, B:E.37, H2O.7, H2O.8
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 10 residues within 4Å:- Chain A: A.1, H.4, D.30, L.180, Q.181, R.182, Y.210, P.211, E.265
- Ligands: TRS.13
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.181
- Water bridges: A:A.183
EDO.6: 5 residues within 4Å:- Chain A: R.7, F.9, Y.28, D.30, D.31
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.31
EDO.7: 8 residues within 4Å:- Chain A: M.6, Y.8, Q.64, Y.160, E.164, S.168, Y.172
- Ligands: MYR.23
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Y.160, A:S.168, A:Y.172, A:Y.172
- Water bridges: A:Y.8
EDO.8: 5 residues within 4Å:- Chain A: G.238
- Chain B: S.53, L.66, Y.68
- Ligands: EDO.10
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.238
- Water bridges: A:Q.33
EDO.9: 2 residues within 4Å:- Chain A: E.59, Y.60
No protein-ligand interaction detected (PLIP)EDO.10: 5 residues within 4Å:- Chain A: Y.28, P.236
- Chain B: S.53, Y.64
- Ligands: EDO.8
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:S.53, B:S.53, A:Y.28
- Water bridges: B:Y.64
EDO.11: 4 residues within 4Å:- Chain A: R.36, E.47, P.48, R.49
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.49
EDO.12: 5 residues within 4Å:- Chain A: R.7, M.99, Y.114
- Chain B: K.59
- Ligands: EDO.16
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.7
EDO.16: 8 residues within 4Å:- Chain A: F.9, M.99, Q.116
- Chain B: F.57, S.58, K.59, W.61
- Ligands: EDO.12
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:S.58
EDO.17: 10 residues within 4Å:- Chain A: W.205, L.207, R.235, Q.243
- Chain B: Y.11, S.12, R.13, H.14, P.15
- Ligands: EDO.18
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:S.12, B:H.14, A:R.235
EDO.18: 5 residues within 4Å:- Chain A: W.205
- Chain B: P.15, P.16, M.100
- Ligands: EDO.17
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:M.100, B:M.100
EDO.19: 4 residues within 4Å:- Chain A: R.22
- Chain B: S.34, D.35
- Ligands: EDO.20
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:S.34
EDO.20: 8 residues within 4Å:- Chain A: I.24
- Chain B: H.52, S.53, D.54, L.55, L.65
- Ligands: EDO.19, EDO.21
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:L.55, A:R.22
EDO.21: 4 residues within 4Å:- Chain A: R.22
- Chain B: H.52
- Ligands: ZN.14, EDO.20
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Water bridges: B:H.52, A:R.36
- Hydrogen bonds: A:R.22
EDO.22: 2 residues within 4Å:- Chain B: E.37
- Ligands: ZN.15
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.37, B:N.84
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 1 x MYR: MYRISTIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Morita, D. et al., Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex. Nat Commun (2016)
- Release Date
- 2016-01-13
- Peptides
- Major histocompatibility complex class I: A
Beta-2-microglobulin: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.76 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 1 x GLY- GLY- ALA- ILE- SER: 5-mer lipopeptide from Protein Nef(Non-covalent)
- 5 x ZN: ZINC ION(Non-covalent)
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 1 x MYR: MYRISTIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Morita, D. et al., Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex. Nat Commun (2016)
- Release Date
- 2016-01-13
- Peptides
- Major histocompatibility complex class I: A
Beta-2-microglobulin: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
E