This entry has been superseded by
5TIQ
on Dec. 21, 2017, midnight.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.55 Å
- Oligo State
- homo-hexamer
- Ligands
- 18 x NAG: SUGAR (N-ACETYL-D-GLUCOSAMINE)(Non-covalent)
- 72 x MAN: SUGAR (ALPHA-D-MANNOSE)(Non-covalent)(Non-functional Binders)
MAN.2: 5 residues within 4Å:- Chain A: T.391
- Ligands: NAG.1, MAN.4, MAN.5, NAG.13
Protein-ligand interaction information (PLIP) not availableMAN.3: 3 residues within 4Å:- Ligands: NAG.1, MAN.4, MAN.5
Protein-ligand interaction information (PLIP) not availableMAN.4: 5 residues within 4Å:- Chain A: A.291
- Ligands: NAG.1, MAN.2, MAN.3, MAN.5
Protein-ligand interaction information (PLIP) not availableMAN.5: 3 residues within 4Å:- Ligands: MAN.2, MAN.3, MAN.4
Protein-ligand interaction information (PLIP) not availableMAN.6: 9 residues within 4Å:- Chain A: N.81, G.82, N.138, L.140
- Ligands: NAG.7, MAN.8, MAN.10, MAN.11, MAN.91
Protein-ligand interaction information (PLIP) not availableMAN.8: 4 residues within 4Å:- Ligands: MAN.6, MAN.10, MAN.11, MAN.91
Protein-ligand interaction information (PLIP) not availableMAN.10: 4 residues within 4Å:- Ligands: MAN.6, NAG.7, MAN.8, MAN.11
Protein-ligand interaction information (PLIP) not availableMAN.11: 4 residues within 4Å:- Ligands: MAN.6, NAG.7, MAN.8, MAN.10
Protein-ligand interaction information (PLIP) not availableMAN.14: 1 residues within 4Å:- Ligands: NAG.13
Protein-ligand interaction information (PLIP) not availableMAN.15: 3 residues within 4Å:- Ligands: NAG.1, MAN.44, MAN.46
Protein-ligand interaction information (PLIP) not availableMAN.16: 5 residues within 4Å:- Chain A: A.394, G.398
- Chain C: V.141, G.142
- Ligands: NDG.12
Protein-ligand interaction information (PLIP) not availableMAN.17: 1 residues within 4Å:- Ligands: NDG.12
Protein-ligand interaction information (PLIP) not availableMAN.19: 4 residues within 4Å:- Ligands: NAG.18, MAN.21, MAN.22, NDG.30
Protein-ligand interaction information (PLIP) not availableMAN.20: 2 residues within 4Å:- Ligands: NAG.18, MAN.21
Protein-ligand interaction information (PLIP) not availableMAN.21: 6 residues within 4Å:- Chain B: T.290, A.291
- Ligands: NAG.18, MAN.19, MAN.20, MAN.22
Protein-ligand interaction information (PLIP) not availableMAN.22: 2 residues within 4Å:- Ligands: MAN.19, MAN.21
Protein-ligand interaction information (PLIP) not availableMAN.23: 8 residues within 4Å:- Chain B: N.81, G.82, N.138, L.140
- Ligands: NDG.24, MAN.25, MAN.27, MAN.70
Protein-ligand interaction information (PLIP) not availableMAN.25: 3 residues within 4Å:- Ligands: MAN.23, MAN.28, MAN.70
Protein-ligand interaction information (PLIP) not availableMAN.27: 3 residues within 4Å:- Ligands: MAN.23, NDG.24, MAN.28
Protein-ligand interaction information (PLIP) not availableMAN.28: 4 residues within 4Å:- Chain B: A.292
- Ligands: NDG.24, MAN.25, MAN.27
Protein-ligand interaction information (PLIP) not availableMAN.31: 1 residues within 4Å:- Ligands: NDG.30
Protein-ligand interaction information (PLIP) not availableMAN.32: 3 residues within 4Å:- Ligands: NAG.18, MAN.99, MAN.101
Protein-ligand interaction information (PLIP) not availableMAN.33: 6 residues within 4Å:- Chain B: A.394, G.398
- Chain F: L.140, V.141
- Ligands: NAG.29, MAN.34
Protein-ligand interaction information (PLIP) not availableMAN.34: 2 residues within 4Å:- Ligands: NAG.29, MAN.33
Protein-ligand interaction information (PLIP) not availableMAN.40: 5 residues within 4Å:- Chain C: T.391
- Ligands: NAG.39, MAN.42, MAN.43, NAG.51
Protein-ligand interaction information (PLIP) not availableMAN.41: 3 residues within 4Å:- Ligands: NAG.39, MAN.42, MAN.43
Protein-ligand interaction information (PLIP) not availableMAN.42: 5 residues within 4Å:- Chain C: A.291
- Ligands: NAG.39, MAN.40, MAN.41, MAN.43
Protein-ligand interaction information (PLIP) not availableMAN.43: 3 residues within 4Å:- Ligands: MAN.40, MAN.41, MAN.42
Protein-ligand interaction information (PLIP) not availableMAN.44: 9 residues within 4Å:- Chain C: N.81, G.82, N.138, L.140
- Ligands: MAN.15, NAG.45, MAN.46, MAN.48, MAN.49
Protein-ligand interaction information (PLIP) not availableMAN.46: 4 residues within 4Å:- Ligands: MAN.15, MAN.44, MAN.48, MAN.49
Protein-ligand interaction information (PLIP) not availableMAN.48: 4 residues within 4Å:- Ligands: MAN.44, NAG.45, MAN.46, MAN.49
Protein-ligand interaction information (PLIP) not availableMAN.49: 4 residues within 4Å:- Ligands: MAN.44, NAG.45, MAN.46, MAN.48
Protein-ligand interaction information (PLIP) not availableMAN.52: 1 residues within 4Å:- Ligands: NAG.51
Protein-ligand interaction information (PLIP) not availableMAN.53: 3 residues within 4Å:- Ligands: NAG.39, MAN.82, MAN.84
Protein-ligand interaction information (PLIP) not availableMAN.54: 5 residues within 4Å:- Chain C: A.394, G.398
- Chain E: V.141, G.142
- Ligands: NDG.50
Protein-ligand interaction information (PLIP) not availableMAN.55: 1 residues within 4Å:- Ligands: NDG.50
Protein-ligand interaction information (PLIP) not availableMAN.57: 4 residues within 4Å:- Ligands: NAG.56, MAN.59, MAN.60, NDG.68
Protein-ligand interaction information (PLIP) not availableMAN.58: 2 residues within 4Å:- Ligands: NAG.56, MAN.59
Protein-ligand interaction information (PLIP) not availableMAN.59: 6 residues within 4Å:- Chain D: T.290, A.291
- Ligands: NAG.56, MAN.57, MAN.58, MAN.60
Protein-ligand interaction information (PLIP) not availableMAN.60: 2 residues within 4Å:- Ligands: MAN.57, MAN.59
Protein-ligand interaction information (PLIP) not availableMAN.61: 8 residues within 4Å:- Chain D: N.81, G.82, N.138, L.140
- Ligands: NDG.62, MAN.63, MAN.65, MAN.108
Protein-ligand interaction information (PLIP) not availableMAN.63: 3 residues within 4Å:- Ligands: MAN.61, MAN.66, MAN.108
Protein-ligand interaction information (PLIP) not availableMAN.65: 3 residues within 4Å:- Ligands: MAN.61, NDG.62, MAN.66
Protein-ligand interaction information (PLIP) not availableMAN.66: 4 residues within 4Å:- Chain D: A.292
- Ligands: NDG.62, MAN.63, MAN.65
Protein-ligand interaction information (PLIP) not availableMAN.69: 1 residues within 4Å:- Ligands: NDG.68
Protein-ligand interaction information (PLIP) not availableMAN.70: 3 residues within 4Å:- Ligands: MAN.23, MAN.25, NAG.56
Protein-ligand interaction information (PLIP) not availableMAN.71: 6 residues within 4Å:- Chain B: L.140, V.141
- Chain D: A.394, G.398
- Ligands: NAG.67, MAN.72
Protein-ligand interaction information (PLIP) not availableMAN.72: 2 residues within 4Å:- Ligands: NAG.67, MAN.71
Protein-ligand interaction information (PLIP) not availableMAN.78: 5 residues within 4Å:- Chain E: T.391
- Ligands: NAG.77, MAN.80, MAN.81, NAG.89
Protein-ligand interaction information (PLIP) not availableMAN.79: 3 residues within 4Å:- Ligands: NAG.77, MAN.80, MAN.81
Protein-ligand interaction information (PLIP) not availableMAN.80: 5 residues within 4Å:- Chain E: A.291
- Ligands: NAG.77, MAN.78, MAN.79, MAN.81
Protein-ligand interaction information (PLIP) not availableMAN.81: 3 residues within 4Å:- Ligands: MAN.78, MAN.79, MAN.80
Protein-ligand interaction information (PLIP) not availableMAN.82: 9 residues within 4Å:- Chain E: N.81, G.82, N.138, L.140
- Ligands: MAN.53, NAG.83, MAN.84, MAN.86, MAN.87
Protein-ligand interaction information (PLIP) not availableMAN.84: 4 residues within 4Å:- Ligands: MAN.53, MAN.82, MAN.86, MAN.87
Protein-ligand interaction information (PLIP) not availableMAN.86: 4 residues within 4Å:- Ligands: MAN.82, NAG.83, MAN.84, MAN.87
Protein-ligand interaction information (PLIP) not availableMAN.87: 4 residues within 4Å:- Ligands: MAN.82, NAG.83, MAN.84, MAN.86
Protein-ligand interaction information (PLIP) not availableMAN.90: 1 residues within 4Å:- Ligands: NAG.89
Protein-ligand interaction information (PLIP) not availableMAN.91: 3 residues within 4Å:- Ligands: MAN.6, MAN.8, NAG.77
Protein-ligand interaction information (PLIP) not availableMAN.92: 5 residues within 4Å:- Chain A: V.141, G.142
- Chain E: A.394, G.398
- Ligands: NDG.88
Protein-ligand interaction information (PLIP) not availableMAN.93: 1 residues within 4Å:- Ligands: NDG.88
Protein-ligand interaction information (PLIP) not availableMAN.95: 4 residues within 4Å:- Ligands: NAG.94, MAN.97, MAN.98, NDG.106
Protein-ligand interaction information (PLIP) not availableMAN.96: 2 residues within 4Å:- Ligands: NAG.94, MAN.97
Protein-ligand interaction information (PLIP) not availableMAN.97: 6 residues within 4Å:- Chain F: T.290, A.291
- Ligands: NAG.94, MAN.95, MAN.96, MAN.98
Protein-ligand interaction information (PLIP) not availableMAN.98: 2 residues within 4Å:- Ligands: MAN.95, MAN.97
Protein-ligand interaction information (PLIP) not availableMAN.99: 8 residues within 4Å:- Chain F: N.81, G.82, N.138, L.140
- Ligands: MAN.32, NDG.100, MAN.101, MAN.103
Protein-ligand interaction information (PLIP) not availableMAN.101: 3 residues within 4Å:- Ligands: MAN.32, MAN.99, MAN.104
Protein-ligand interaction information (PLIP) not availableMAN.103: 3 residues within 4Å:- Ligands: MAN.99, NDG.100, MAN.104
Protein-ligand interaction information (PLIP) not availableMAN.104: 4 residues within 4Å:- Chain F: A.292
- Ligands: NDG.100, MAN.101, MAN.103
Protein-ligand interaction information (PLIP) not availableMAN.107: 1 residues within 4Å:- Ligands: NDG.106
Protein-ligand interaction information (PLIP) not availableMAN.108: 3 residues within 4Å:- Ligands: MAN.61, MAN.63, NAG.94
Protein-ligand interaction information (PLIP) not availableMAN.109: 6 residues within 4Å:- Chain D: L.140, V.141
- Chain F: A.394, G.398
- Ligands: NAG.105, MAN.110
Protein-ligand interaction information (PLIP) not availableMAN.110: 2 residues within 4Å:- Ligands: NAG.105, MAN.109
Protein-ligand interaction information (PLIP) not available- 12 x NDG: SUGAR (2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE)(Non-covalent)
NDG.9: 5 residues within 4Å:- Chain A: G.83, D.299, G.301, N.302
- Ligands: NAG.7
Protein-ligand interaction information (PLIP) not availableNDG.12: 8 residues within 4Å:- Chain A: S.387, I.388, D.389, A.395, G.398, N.399
- Ligands: MAN.16, MAN.17
Protein-ligand interaction information (PLIP) not availableNDG.24: 7 residues within 4Å:- Chain B: G.82, G.83, N.138
- Ligands: MAN.23, NAG.26, MAN.27, MAN.28
Protein-ligand interaction information (PLIP) not availableNDG.30: 5 residues within 4Å:- Chain B: D.389, A.390, N.406
- Ligands: MAN.19, MAN.31
Protein-ligand interaction information (PLIP) not availableNDG.47: 5 residues within 4Å:- Chain C: G.83, D.299, G.301, N.302
- Ligands: NAG.45
Protein-ligand interaction information (PLIP) not availableNDG.50: 8 residues within 4Å:- Chain C: S.387, I.388, D.389, A.395, G.398, N.399
- Ligands: MAN.54, MAN.55
Protein-ligand interaction information (PLIP) not availableNDG.62: 7 residues within 4Å:- Chain D: G.82, G.83, N.138
- Ligands: MAN.61, NAG.64, MAN.65, MAN.66
Protein-ligand interaction information (PLIP) not availableNDG.68: 5 residues within 4Å:- Chain D: D.389, A.390, N.406
- Ligands: MAN.57, MAN.69
Protein-ligand interaction information (PLIP) not availableNDG.85: 5 residues within 4Å:- Chain E: G.83, D.299, G.301, N.302
- Ligands: NAG.83
Protein-ligand interaction information (PLIP) not availableNDG.88: 8 residues within 4Å:- Chain E: S.387, I.388, D.389, A.395, G.398, N.399
- Ligands: MAN.92, MAN.93
Protein-ligand interaction information (PLIP) not availableNDG.100: 7 residues within 4Å:- Chain F: G.82, G.83, N.138
- Ligands: MAN.99, NAG.102, MAN.103, MAN.104
Protein-ligand interaction information (PLIP) not availableNDG.106: 5 residues within 4Å:- Chain F: D.389, A.390, N.406
- Ligands: MAN.95, MAN.107
Protein-ligand interaction information (PLIP) not available- 12 x HG: MERCURY (II) ION(Non-covalent)
HG.35: 5 residues within 4Å:- Chain A: L.320, F.356, C.369, F.371, I.374
Protein-ligand interaction information (PLIP) not availableHG.36: 5 residues within 4Å:- Chain A: P.241, A.243, C.386, N.406, T.409
Protein-ligand interaction information (PLIP) not availableHG.37: 6 residues within 4Å:- Chain B: P.241, S.242, A.243, C.386, N.406, T.409
Protein-ligand interaction information (PLIP) not availableHG.38: 5 residues within 4Å:- Chain B: L.320, F.356, C.369, F.371, I.374
Protein-ligand interaction information (PLIP) not availableHG.73: 5 residues within 4Å:- Chain C: L.320, F.356, C.369, F.371, I.374
Protein-ligand interaction information (PLIP) not availableHG.74: 5 residues within 4Å:- Chain C: P.241, A.243, C.386, N.406, T.409
Protein-ligand interaction information (PLIP) not availableHG.75: 6 residues within 4Å:- Chain D: P.241, S.242, A.243, C.386, N.406, T.409
Protein-ligand interaction information (PLIP) not availableHG.76: 5 residues within 4Å:- Chain D: L.320, F.356, C.369, F.371, I.374
Protein-ligand interaction information (PLIP) not availableHG.111: 5 residues within 4Å:- Chain E: L.320, F.356, C.369, F.371, I.374
Protein-ligand interaction information (PLIP) not availableHG.112: 5 residues within 4Å:- Chain E: P.241, A.243, C.386, N.406, T.409
Protein-ligand interaction information (PLIP) not availableHG.113: 6 residues within 4Å:- Chain F: P.241, S.242, A.243, C.386, N.406, T.409
Protein-ligand interaction information (PLIP) not availableHG.114: 5 residues within 4Å:- Chain F: L.320, F.356, C.369, F.371, I.374
Protein-ligand interaction information (PLIP) not available- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nandhagopal, N. et al., The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. Proc.Natl.Acad.Sci.USA (2002)
- Release Date
- 2002-11-20
- Peptides
- Major capsid protein: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B
SMTL ID : 1j5q.1 (2 other biounits)
The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.
Major capsid protein
Toggle Identical (ABCDEF)Related Entries With Identical Sequence
6ncl.30 | 6ncl.31 | 6ncl.32 | 6ncl.33 | 6ncl.34 | 6ncl.35 | 6ncl.36 | 6ncl.37 | 6ncl.38 | 6ncl.39 | 6ncl.40 | 6ncl.41 | 6ncl.42 | 6ncl.43 | 6ncl.44 | 6ncl.45 | 6ncl.46 | 6ncl.47 | 6ncl.48 | 6ncl.49 | 6ncl.50 | 6ncl.51 | 6ncl.52 | 6ncl.53 | 6ncl.54 | 6ncl.55 | 6ncl.56 | 6ncl.57 | 6ncl.58 | 6ncl.59 more...less...6ncl.60 | 6ncl.61 | 6ncl.62 | 6ncl.63 | 6ncl.64 | 6ncl.65 | 6ncl.66 | 6ncl.67 | 6ncl.68 | 6ncl.69 | 6ncl.70 | 6ncl.71 | 6ncl.72 | 6ncl.73 | 6ncl.74 | 6ncl.75 | 6ncl.76 | 6ncl.77 | 6ncl.78 | 6ncl.79 | 6ncl.80 | 6ncl.81 | 6ncl.82 | 6ncl.83 | 6ncl.84 | 6ncl.85 | 6ncl.86 | 6ncl.87 | 6ncl.88 | 6ncl.89 | 6ncl.90 | 6ncl.91 | 6ncl.92 | 6ncl.93 | 6ncl.94 | 6ncl.95 | 6ncl.96 | 6ncl.97 | 6ncl.98 | 6ncl.99 | 6ncl.100 | 6ncl.101 | 6ncl.102 | 6ncl.103 | 6ncl.104 | 6ncl.105 | 6ncl.106 | 6ncl.107 | 6ncl.108 | 6ncl.109 | 6ncl.110 | 6ncl.111 | 6ncl.112 | 6ncl.113 | 8h2i.1 | 8h2i.2 | 8h2i.3 | 8h2i.4 | 8h2i.5 | 8h2i.6 | 8h2i.7 | 8h2i.8 | 8h2i.9 | 8h2i.10 | 8h2i.11 | 8h2i.12 | 8h2i.13 | 8h2i.14 | 8h2i.15 | 8h2i.16 | 8h2i.17 | 8h2i.18 | 8h2i.19 | 8h2i.20 | 8h2i.21 | 8h2i.22 | 8h2i.23 | 8h2i.24 | 8h2i.25 | 8h2i.26 | 8h2i.27 | 8h2i.28 | 8h2i.29 | 8h2i.30 | 8h2i.31 | 8h2i.32 | 8h2i.33 | 8h2i.34 | 8h2i.35 | 8h2i.36 | 8h2i.37 | 8h2i.38 | 8h2i.39 | 8h2i.40 | 8h2i.41 | 8h2i.42 | 8h2i.43 | 8h2i.44 | 8h2i.45 | 8h2i.46 | 8h2i.47 | 8h2i.48 | 8h2i.49 | 8h2i.50 | 8h2i.51 | 8h2i.52 | 8h2i.53 | 8h2i.54 | 8h2i.55 | 8h2i.56 | 8h2i.57 | 8h2i.58 | 8h2i.59 | 8h2i.60 | 8h2i.61 | 8h2i.62 | 8h2i.63 | 8h2i.64 | 8h2i.65 | 8h2i.66 | 8h2i.67 | 8h2i.68 | 8h2i.69 | 8h2i.70 | 8h2i.71 | 8h2i.72